This is the best I can do at explaining what is involved in doing the R6 fork and brake mod. If I don't do a very good job, forgive me. Writing is not my strongest asset. Keep in mind that my mod incorporates forks from a 2003-2004 R6 and will not work with forks from previous years. I elected to go with the newer '03-'04 forks because I know that those years R6's use the same wheels and rotors as mine and felt that my wheels and rotors stood a much better chance of working hand in hand with the forks that are already matched with them on another bike. The unknown variable was the axle which IS difference from mine. I really only expected the difference to be related to the differences in the axle mounting holes in the forks and to not really matter in any other way and that turned out to be an accurate assumption.
The only real surprise that I faced was that the FZ6 forks are spaced 5 mm further apart and didn't find that out until I was able to physically measure the triple clamp on the forks that I ordered and compare that to the measurements taken from my triple clamp. My initial response was that of doom and gloom because I knew that meant that the calipers were also going to be out of sync with the rotors and shimming, though possible, would be a difficult task and require custom fabricated shims. At that point, I almost gave up on this project as many of you will remember from my work-in-progress posts. Had it not been for the encouragement of other members and re-affirment from others that shimming should be a viable option, I probably would have quit. Instead, I became even more obsessed with making this work and in the end it did. Here is how I did it.
First, what is needed. Below is a list of the parts which I recommend buying for this project. I have place "optional" braided stainless brake lines because it is possible, though unrecommended to do this without them. I purchased all parts used from ebay because of the availability and affordability of such and have listed the prices that I paid for your reference. I might could have gotten better deals had I been patient, but patience is not in my personality. Even still, I got through this mod for $300 and when you consider that the retail of these parts new would cost around $1500, I feel like it was a bargain. I know of another member who bought an entire front end for $200.
What is required:
- 2003/2004 set of R6 forks with calipers.
- 2003/2004 R6 front axle and end bolt.
- Braided stainless brake lines for the FZ6 (optional)
- 19mm Hex Head Axle Removal tool
- 6mm & 8mm Allen head tools for the fork clamp bolts
- adapter kit to shim the axle, calipers and to be able to fit the stock fender back to the new forks. Contact me at mgracer65@hotmail.com and I will hook you up.
The process: This mod can be done without removing the front fairing, so do not do so.
1) You will first need to get the font end off of the ground. I achieved this with nothing more than my center stand and two 55 pound bags of fertilizer placed on the rear passenger seat. Make sure to put the bike in 1st gear and roll the
2) Remove the front fender and brake line mounting blocks wheel as far forward as possible so that it will not have a chance to roll off of the center stand. You must also be working on a hard surface such as cement or asphalt. Use the center stand and a car scissor jack under the exhaust pipes near the front. The center stand and rear wheel take most of the load, the jack just pushes the balance to the rear wheel. it works great.

3) Remove the front brake calipers by removing the two bolts that attach each one to the forks and pulling the up and away from the rotors. You could detatch them from the brake lines at this time or later. I waited until later because I didn't want fluid dripping while I was working. If you do it later, you can use a piece of wire or string to tie the back out of your way.
4) Use the 19 mm axle removal tool to take out the axle. Mine was torqued very tight and required a rubbler mallet to hit on the ratchet to get it started. It threads in and out in a normal direction for bolts. Counter clockwise to remove.
5) Remove the front wheel and set it aside. Pay attention to the fact that the tire has a directional arrow so that you put it back on in the right direction.
6) Loosen the top triple clamp bolts on both sides, and then loosen the lower triple clamp bolts one at a time. Make certain that you have one hand on a fork when loosening the lower clamps so that it doesn't slip out and fall to the ground.
7) Slide the new R6 forks into the clamps from the bottom, one at a time. The forks are only meant to go on a specific side and the clue to look for is this....the caliper mounting tabs always go towards the rear and the numbers that are stamped on them always are to the inside facing the wheel. The smooth side of the forks are to the outside where they are seen. Push the forks up until the top is flush with the top of the upper clam. The blue adjuster and the silver cap will both be showing above the clamp. Tighten either the upper or lower clamp bolt to keep the fork from falling out. Install the other fork the same way and tighten all clamp bolts very tightly. You can refer to the manual for torque numbers if you have a torque wrench, but get them as tight as you can with an allen wrench and that should be fine
Tip for all:
While the front end change does upgrade the suspension, it does throw off the CG just a little. The CG which was designed for by the engineers... especially for me with the naked conversion and all of the wieght from the front I have lost. Anyway - the tip is this. Lower the front end in the forks about 3.5mm - 5mm and you will notice and huge increase in stablity and dive. The way to check if you need to do this. Look at the "chicken strips" on the front tire. If you can't get the bike to dive so you can ride to almost the edge of the front tire, then you need to lower the front so the bike will have more suspension use in the front, which is where you just spent all this money. You need to move the fork up or move the triple down so that there is 3.5-5mm spacing between the alignment line on the R6 fork and the top of the triple. I used a 3.5mm allen key on it's side to measure so I could line them up the same on both sides. Also - it's easy, but a bit of a task to do. I needed another person to help, and you do one side at a time.
Steps I used were to loosen bottom pinch bolt, then have someone hold the front end with you as you loosen the top pinch bolt really slowly to the point the fork just starts sliding - then tighten it when you get to the right point.
Tighten top, tighten bottom, do the other side. I had mine set at 5/8" and they worked beautifully. Very stable and well handling. Never squirrelly. I wouldn't go any more than that because the forks will bottom out on the lower

tripple clamp at around 1".You know what I just realized? We are talking about the same thing. duhhhh. The pic you show is when I had the forks flush (at the line). If that is where you started, then what he told you is to drop them roughly 1/4". That is standard procedure. Always do no more than 1/4" drop at one time.... I'm just telling you that had you dropped them even more, you would have prolly liked it even better. Measuring from the top of the tubes
(not the tube covers) it looks like 7/16" difference. Because of the differences in the spring rates (42.25 lb/in - FZ6 to
47.39 lb/in - R6), the R6 forks have to be raised up slightly in the upper triple, even though they are shorter to begin with. Others have posted up the amount of fork tube they raised above the upper triple to be somewhere around
1/2", but I went with 1/4". I don't know exactly how everyone else got their #'s, but I used an estimated total weight of 600 lbs for the vehicle and rider, and assumed a 50/50 weight distribution (should be close). The FZ6 would then compress around 11/16" more than the R6 (I used the force vector along the fork tube - i.e. weight*cos(24 degrees)
- to calculate the static sag). So I went with 11/16" - 7/16" = 1/4". I should add that I measured the amount of fork tube sticking above the upper triple from the top of the fork tube down to the triple, not from the top of the cap/cover on the fork tube. These are different thicknesses between the two sets of forks, so I thought that the top of the tube itself was a more accurate comparison.
175 lbs - 4 lines showing for the preload, and 2 clicks back from the bottom for rebound and comp damping. motorcycle issue front preload front rebound damping front comp. damping rear preload rear rebound damping rear comp. damping
YZF-R6
('04)
8/04
7 lines showing
1 click out
11 clicks out position 5 of 9 2 clicks out 10 clicks out note: set fork tube height to 10mm showing above flat portion of bar clamp with Dunlop D208 GP-A tires
8) Begin to push the R6 axle through the fork on your right side as you are facing the front of the bike. It will only fit one way. When you see it pop throught the fork, slide a .090" shim (I have made some of them for you guys) onto the axle and then position the wheel with the wheel spacers already in place, into the forks, aligned so that the axle will shove through it. Once the axle pushes through the wheel and spacer on the other side, you will need to slip the other shim in between the wheel spacer and the fork and push the axle the rest of the way through the fork on your left. Screw in the bolt that fits in the end of the axle. It will go throught the fork on your left and thread into the axle which is inside the hole of that fork. Tighten this bolt very snugg. You can now tighten the pinch bolts at the bottom of the fork to lock the axle in place. The end of the axle on the right side should be flush with the outside edge of the fork and there be NO side to side movement of the wheel. If there is any movement side to side, then loosen the pinch bolts on the right side, lightly snugg one of them, and then tap in on the right fork with a rubber mallet to push everything tight. Then tighten the pinch bolts fully. I just tightened up the regular hex bolt on the right side of the bike and there was enough friction that I didn't need to secure the other side (the internal 19mm hex side). After that, you tighten up the two small allen screws on the bottom of each fork. "Secure the wheel axle by installing the axle bolt, and then tightening it to the specified. the R6 axle is inserted from the opposite side as the
FZ6 axle was. I was wondering if L and R on the forks were from a different point of reference, but the pictures in this thread showed that I had them on correctly. Torque the allen head is for get it good and tight. The pinch bolts really are what hold the axle in place anyway. By the way in case anybody cares to know, the axle end bolt is 22mm.
Axle bolt: 91 Nm (9.1 mkg, 66 ftlb removing the fz6 axle. just use your socket on the axle nut and use a torque wrench. If you don't hava a torque wrench then just

9) The new calipers will need to be installed next using a shim between the caliper and forks. There will need to be a shim for each mounting point (two per caliper). Again, I have made some of those which I can supply you. the calipers will only fit one way so getting it right shouldnt be too tough. The left only fits the left and right fits the right. Tighten the mounting bolts very tight.
10) At this point, you are ready to attach the brake lines and bleed the brakes using the proper method that is stated in the service manual. If you are fitting new lines, be very careful not to get fluid on any of your painted surfaces.
One other thing is important. If using your stock brake lines, you will need to disconnect the line from the master cylinder and turn it around so that the fitting takes a better angle away from the reservoir. I highly recomend new duel braided lines because the stock lines will be a much tighter fit as the distance from the mastercylinder to the calipers is about an inch longer than before. Besides, if upgrading the brake calipers to R6 specs, why would you want to use a single line rubbler brake line? It dosn't really make practical sense. I had them put strait end on all ends except the longer of the 2 lines I had them put a offset so when you put them together at the master cylinder it would fit better You should see what I am talking about in the pictures below.

If you still feel sponginess, I'd suggest bleeding your lines again. There may be some air in the lines still. Spongy means air. Bleed them some more. I like to wrap teflon tape around the bleeder valve threads to keep air from sucking back in past them. Even with your rubber hose submerged in fluid, air will slip back in past those threads until the bleeder is closed tight. The tape will eliminate that. Once all the air is out, the brake lever will feel just as firm as before but the stopping power will be much stronger. the guy I got my forks from was a racer and he told me that for my weight, try 4 lines showing for the preload, and 2 clicks back from the bottom for rebound and comp damping. Feels great to me. I weigh 175, so use that as a start and go from there.

Step (1)
Step (2)
Step (3)
Step (4)
It's been a couple of years, maybe, and the fluid in the eye of the clutch-side reservoir looks more like mocha java than peachy chardonnay. Time for a flush-and-bleed job on the old hydraulic-clutch system?
Relax. It's a closed hydraulic system, just like the front and rear brakes.
But why is the fluid brown (1)? The petroleum-based goo labeled DOT
3 or DOT 4 is hygroscopic, which means it absorbs water. That water eventually turns the fluid brown in a sort of plain-to-see maintenance check. Flat beer means replace the keg. Same deal here.
There are other reasons to give a hydraulic clutch some attention. Is the level in the reservoir going down quickly? Check the seal around the actuator. This guy lives in a tough environment--with the rubber Oring that seals the slave cylinder contending with engine heat, road grime, excess chain lube and myriad other evils. Maybe the engagement point of the clutch moves erratically, or according to changes in the weather. Before you buy new clutch plates, check the actuating system.
Let's get on with it, then. You don't want more crummy DOT 3 or
DOT 4 running through the system, so carefully evacuate the reservoir
(2). We use those cheap nasal aspirators--parents know to look for these between the tippy cups and the Bag Balm--to suck out the goop.
Then refill the reservoir with fresh fluid (3). Check the condition of the brake fluid you're using, too. Fluid left sitting in a previously opened container can be as contaminated as what you're trying to replace. So splurge: buy a new bottle.
Step (5)

Shift your attention to the slave cylinder. Sling your box-end wrench over the bleeder nipple and attach a length of clear plastic hose (4). Drop the free end of the hose in a suitable container (5).
Step (6)
Reach up and pump the clutch lever two or three times and then hold it to the bar (6). Crack the fitting (7); open it just enough to allow the fluid to move into the hose. It may take some time to know when to close the bleeder screw again. Unlike a brake system, there'll be no feedback at the lever to let you know when line pressure drops. Watch the hose carefully and close the bleeder an instant before you think the fluid will stop moving. If you don't, air bubbles and assorted grunge can be dragged back into the system through the bleeder.
Step (7)
Continue watching the hose until you see a change in the color of the fluid (8). Sometimes it's subtle--at least it will be if you haven't let this job go for too long. Keep bleeding the system in steps. Grip the clutch lever and pump two or three times, crack the bleeder screw, watch the line for bubbles, then close. Rinse and repeat for a healthy, shiny coat.
Step (8)
Step (9)
Track fluid level in the reservoir throughout the procedure. Suck air into the system now and you've got to start all over again.
Once all the old fluid and air bubbles are gone, fill the reservoir according to the markings (9). Because it's possible for the clutch lever to feel firm with air in the system, which will not allow the clutch to fully disengage, test your work by putting the bike in gear with the engine off. See if the clutch disengages enough to let the bike roll slightly. Wet clutches are grippy until the engine is running, but you should still be able to feel the difference.
Finally, make double-sure the bleeder fitting is tight and you've cleaned up any spilled fluid because DOT 3 and DOT 4 are corrosive.
Mityvac Vacuum Brake Bleeder ATE Super Blue Brake Fluid
You use an air compressor to clear out a caliper and youll blow the pistons out of it. Most people cant take a caliper apart and put it together without making a big leak. Clean fluid is fine, the fluid will get dirty almost immediately anyways and it absorbs moisture from the air as well. Brake fluid is hydroscopic meaning it is really attracted to water and will pull it from anywhere it can. Old brake fluid (6 months) should be discarded IF THE TOP HAS BEEN POPPED.
Completely draining the system before filling with new fluid is asking to get air in the lines or calipers. I flush mine by pumping the brake levers while letting it out of the bleed valve while adding new fluid until only clean fluid comes out.
Its not hard to pump and twist a wrench on the bleeder at the same time. Just watch the fluid level and refill as necessary. I replaced, filled, and bleed all three hydraulic lines on my RC by myself. Most of the time was spent carefully evacuating the old fluid beforehand and ripping the OEM lines off. If you let the reservoir go dry, you have to start over. its probably a good idea to flush about half a bottle thru the lines to help push out any tiny bubbles that can accumulate. vibrations can cause them to collect and give ya soft brakes. Just get some small platic tubing to fit over the bleed valves

for the fluid and catch it in a can or bottle (clean it if ya wanna reuse the fluid and keep bleeding). Bleeding is easy. I used a rubber line I already had- cut it in 2- put one firmly on the end of each nipple- pumped the brake 10 times and held it in on the last one- opened the nipple valve for 2 seconds, letting the bubbles out, and kept bleeding them until the fluid in the tubes turned clear again. Takes 6 minutes. Its great being able to control the brake and the valve all by yourself. It should only take 3 crush washers on the Master cylindar, and 2 on the calipers. Are you pumping the break, then opening the bleeder valve for a second or two, then shutting the valve before releasing the brake lever? With the new lines and calipers, it will take awhile to get the fluid pumped through the lines and into the calipers. It takes a long time to get the fluid through the lines and behind the pistons. Fill the reservoir and put the cap back on. Tighten the bleed screws on each caliper. Then, pump the brake lever several times until it is tight, and hold it in while you release then retighten ONE of the bleed screws. Do this process several times, making sure to check the reservoir level and top it off each time. After several times, move to the other caliper and repeat this same process. It took forever for the lever to start feeling tight after pumping it for me. Even when it wasnt feeling tight, I would just simply pull the lever in, open the bleeder valve for a second, close the bleeder valve, release the lever. Repeat about 50 times, making sure the reservoir is empty. As long as your reservoir is emptying using the above method, then your good. It just takes a bit of time to work all that fluid down into the new lines, and into the calipers. It took me roughly 2-3 hours to get the brakes into proper working order.
A tip for when you are done- use q-tips and place them inside the bleed screw opening overnight before placing the rubber dust cap back on them. The bleed screw will hold a small amount of brake fluid in that hole after you close them, and that will leak out during your first ride. It's not alot, but enough to make you think things aren't torqued down enough.
To bleed them, open the bleeders and connect a clear piece of tubing....pump the brakes until all the fluid is out.
Replace the lines and fll the master cylendar (never let it go dry or else you have to start over). Open the bleeder and pump them up a bit (will have to do this to both calipers). Open the bleeders barely to let the air out of the lines and then tighten down and pump them some more. Keep doing this until there are no air bubbles. A vacum pump would help speed things up. If you do this and the brakes don't pump up, check on the MC and see if there is a bleeder there too and do the same. you cant pump the lines with the bleeder open or it'll just suck air back in thru the bleeder. the idea of clear tubing is awesome because you can see when the air bubbles exit the system; thus allowing you to view when no more air bubbles are exiting. On each caliper is the bleeding nipples (hehe, I said nipples). That is where you want to put your wrench (the 8 mm I believe). Put the closed end of the wrench over the nipple, attach the hose, follow the above the procedure.
I like to drop the free end of the hose into a clear clean pop bottle (like a 20 oz or something) so that when I am finished,
I can cap and take it to a disposal facility and it is self contained, without danger of leaking. The biggest, most important thing in effeiciency is not letting the MC run dry. If, once you get finished, the brakes feel mushy, stop and start over over because you have air in there. That lever should feel hard and you shouldn't have to mash on it to get complete braking power.
-pump up the brakes
-open bleeder slightly while keeping pressure on the brake lever
-close bleeder before reaching the end of the stroke on the lever
-repeat
To bleed them, open the bleeders and connect a clear piece of tubing....pump the brakes until all the fluid is out.
Replace the lines and fll the master cylendar (never let it go dry or else you have to start over). Open the bleeder and pump them up a bit (will have to do this to both calipers). Open the bleeders barely to let the air out of the lines and then tighten down and pump them some more. Keep doing this until there are no air bubbles. put the wrench on the bleeder screw BEFORE putting the clear line on
I think the biggest concern when doing brakes is to take care that you've covered the body panels/fenders and anything that you would not want to spill fluid on. Gather the fluid, towels, and anything else you need before you even take the cap odd the reservoir. Be careful not to push/pull the front wheel around too hard when you do have the reservoir cap open. On the banjo bolt going into the front master cylender, don't over tighten or it will snap right half. it helps to

submerge the other end in a little bit of brake fluid, so incase you let off teh brake too early, you wont get as much air in the lines and have to start over
Steps for bleeding all NON-ABS brakes with speedbleeders.
1) Open the reservoir cover.
2) Find the bleeder screw (you should have already replaced it with a speedbleeder, just remove the old and insert the new).
3) Attach a bleed hose to the screw, ensure the hose drains into a safe plastic container.
3) Turn the bleeder screw 1/4 turn, just as you would a normal bleeder screw.
4) While keeping a VERY careful eye on the level in the reservoir, begin to gently pump the brake lever. You should see brake fluid start to fill the hose.
5) When the reservior gets to about 1/4 full, add more until its full (NEVER RUN THE RESERVOIR ALL THE WAY TO
EMPTY) and continue until it is 1/4 full again. By now, when you pump the lever, you should see NO bubbles in the hose from the evacuating fluid. Fill the reservoir one last time, up to the indicated "fill" line.
6) With the reservior full, close off the bleeder screw tightly.
7) Now, if you squeeze the brake lever, you should feel immediate and firm resistance to any motion of the lever.
8) Replace the reservoir cap, you are done.
The steps for doing this without a speed bleeder are a little more complicated.
1) Open the reservoir cover.
2) Find the OEM bleeder screw.
3) Attach a bleed hose to the screw, ensure the hose drains into a safe plastic container.
4) The procedure for each pump of the lever is as follows:
4a) Squeeze the lever to put firm pressure in the line.
4b) Without changing pressure on the lever, unscrew the bleeder 1/4 turn until the pressure drops and fluid comes out of the tube. DO NOT LET THE LEVER BACK OUT...KEEP THE LEVER FULLY DEPRESSED!!!!
4c) Tighten the bleed screw again, THEN let the lever back to its 'at rest' position.
4d) Repeat 4a-4c for EACH depression of the lever...this is why bleeding brakes is usually a two person job.
5) When the reservior gets to about 1/4 full, add more until its full (NEVER RUN THE RESERVOIR ALL THE WAY TO
EMPTY) and continue until it is 1/4 full again. By now, when you pump the lever, you should see NO bubbles in the hose from the evacuating fluid. Fill the reservoir one last time, up to the indicated "fill" line.
6) With the reservior full, close off the bleeder screw tightly.
7) Now, if you squeeze the brake lever, you should feel immediate and firm resistance to any motion of the lever.

8) Replace the reservoir cap, you are done.
1) When I removed the tank to paint my bike, I had to remove the fuel. I removed the allen head screws that hold the filler cap on, and slid the end of a siphon as far down towards the seat as possible. Once the fuel is removed, there will be a fair bit left at the bottom of the tank. I didn't find an easy way to remove this fuel without spilling it everywhere. I took off the fuel pump and held the tank over a wide bucket and just shook the thing like crazy for a couple minutes. Gas is volatile enough that the rest evaporated before I started any work on the tank.
2) Take your seat off first, then remove the two bolts at the front of the tank by the headstock (if you've got a faired one i think you need to take the two side panels off first) then flip the tank up, i use a old oil container and prop it up on the airbox but anything will do. once the tank is propped up you have to pull out the two breather pipes that run down the right hand side of the bike, they should just pull through but be carefull not to split or break em, you can then just keep’em attached to the tank. Remove the breather hoses and leave them on the bike, this makes it easier to reinstall the tank when it's time. I found I only had to pull the tank up to about a 45 deg. angle before I could get in with pliers to remove those hoses.
breather hoses, 'lectric connections and fuel line still attached
3) Next you have to disconnect the electrical harness for the fuel pump, just pull off the two connectors but remember which is for which. once thats all off its just the fuel line, theres a little clip which holds it on, this just clips off, then you have the fuel line with two "buttons" on the side, pinch these together (you'll know what i mean when you see it) and you can just pull the pipe off, be carefull not to break the connector but you should be ok as long as you dont force it. you will probably spill a little fuel out of the pipe (its just residual, its not gonna start gushing out on you), so just hold it over the side to drain on the floor, if your bothered about spilling it on your bike i suppose you could put a rag under before you disconnect it.

2 electric connectors removed, fuel line still attached. You can see the clip holding it in place. Clip removed, you can see "inside" the connector.
I had a fair bit of fuel spray out of the line when removing it from the tank.. it would be beneficial to have an absorbent spill pad under the tank to catch the drips and prevent them from getting all over your electronics.
4) Next thing to do is carefully place the tank back down and remove the long bolt holding the tank on at the back, after that the tank will just lift off, make sure you've prepared somewhere to place the tank down before you take it off, you cant just lay it flat on the floor as it will rest on and break the fuel pump connector so you have to suspend it on something, i usually get the seat and turn it upside down so the leather is on the ground. i rest the front of the tank on this then use my old oil container to support it at the back, just make sure its stable before you leave it! so there you go, sorted! i just noticed that you live in california and if you have a cal spec bike it may be slightly different! there may be an extra connector and only one of the pipes on the tank (i think its a breather pipe, the other is a fuel overflow and i dont think its on the cal models) just check this out before you start playin'
5) It would be a good idea to wash everything with soap and water after removing the tank, I'm not sure if gas will dry out rubber hoses/seals, but I know it's not great for the paint on the tank, and soap and water will help get rid of that gas station smell!
I finished up the headlight mod and the pod lights (amber LEDs) last night. For the headlight mod, I snipped the green wire by the connector on the right side of the frame by the steering head. (Left side as seen from the standing in front of the bike.) Sitting on the bike, I believe it's on the right side by the steering head. You may have to remove the fairing to get to it. I don't recall, since I had the fairing off at the time for a different project.
That's the connector where the proper wire dead end terminates (the mating connector does not have a wire in that location). That's why it's okay to cut the wire there.
I then sliced a hole in the plastic sleeve on the left side of the bike, and pulled that green wire through. When it was pulled, I soldered on an extension wire with a bullet connector, then wrapped it up in the factory harness, so it exits next

to the factory connector.
On the fairing, I soldered a spade terminal onto a wire and inserted it into the empty H4 headlight socket slot (after enlarging the opening on the terminal). I then ran the wire with the factory harness over to when the factory connectors are.
For the pod lights, I tapped into the two non-ground turn signal wires on each side, so the pod LEDs will function as running lights and turn signals. I chose not to use any disconnects, since the R1 pod light sockets aren't going anywhere.
I don't know if any of this stuff works, since I don't have a battery in my bike yet and the fairing is still off of the bike....
Here are the pictures: (attached instead of linked, so they stay if my site dies)
Attached Thumbnails

The first pic shows where I snipped the dead ended wire at the connector plug. The other side of that connector doesn't have a wire in it, so it wasn't doing anything.
Then from up high, I pulled the wire that I snipped, from the bottom part of the bundle and routed it out from a higher spot. That's the second picture.
I then soldered on a longer wire with a bullet connector to the wired that I just pulled, and ran it over to the connector where the stuff in the fairing plugs in. That's the third and fourth picture.

Finally, I put a new wire and connector into the empty location in the right headlight socket, ran the wire of to the left hand side (with the other wires) and put the other gender bullet connector on the end. This is the last picture.
When I install the fairing, I merely connect the factory harneses and the one extra bullet connector that I added.
Today I went to the garage with:
-2 R1 pod light sockets P# 5PW-84312-00-00
-2 amber LED marker lights JamStrait 194 LED bulbs
-an extra length of black wire,
-a box of crimp on connectors
-some heat shrink tubing
-2 - 5 pin relays
-wiring diagram that I printed from another forum on the subject
I started on the left side. I hooked up my test light to determine which wire was the marker - which was the turn signal wire. I then went to verify that the black was hooked to ground, it was - but I also found that the flasher wire was also hooked to ground when it was inactive. So the flasher wire was switching between 12 volt and ground as it flashed. This gave me an idea. I hooked my test light between the turn signal wire - and the marker light wire. When I turned on the key - the marker light and the test light came on. When I turned on the turn signal - the stock blinker flashed alternated by the test light flashing. It is exactly the behavior people were using relay's for.
The concept is simple - if you put 12 volts on each lead of the pod light (Turn signal flashing) - pod light turns off. If you think of it in other terms - if you put exactly the same amount of water pressure on each end of a water pipe - the water can't flow. The same applies to electricity. When the turn signal wasn't flashing is was connected to ground - and the pod light came on again.
So - I pulled the stock R1 contacts out of the plastic connector. I then cut and extended the stock R1 contacts so they would reach the back side of the stock FZ6 turn/marker connector. I used the shrink tubing to insulate the exposed R1 connector - leaving some of the contact sticking out. I then simply slid the exposed end of the R1 terminal into the back side of the FZ6 connector. Zip tied the connections in place. Done! Works like a charm. Don't need to modify the stock wiring at all - don't even need to disconnect the stock wiring for that matter. Couldn't be easier.
Now all I have to do is bring my relays, and the crimp connectors back to the store and get my money back!
Here is a write up on how to replace the fork seal and it has the info you need. In your case you did not set the relative distance from the fork cap to the end of the dampener rod correctly. See steps 9,10 in the Procedure and 9&10 in the fork assembly section. Better yet read the whole thing 2X
As your fork oil should be changed at 10k this may help.
Remember the upside down forks need a spring compressor to replace the oil.
Fork oil/seal replacement

This guide should help the user in replacing the fork oil, fork spring and fork seals.
As always this is just a guide, consult your maintenance manual for specific instructions as if you do not perform this procedure correctly you may get injured.
Procedure:
1 Loosen all of the hardware that will need to be removed
2 Place bike on rear stand and then lift front wheel off ground
3 Important: Top triple clamp must be loose before loosening the top fork nut. Loosen top fork nut.
4 Remove front brakes, wheel and fender
5 Loosen clip on’s
6 Loosen lower triple clamp
7 Remove fork
8 Repeat steps 6-7 for other fork
9 Using screwdriver unscrew the rebound dampener screw to it’s full up position (counterclockwise). Do this gently or you will ruin the screw.
10 Once the screw gently tops out count turns or click while screwing in the dampener screw until it gently bottoms out.
Do not omit this step, write down the number of turns or clicks. Unscrew the rebound dampener screw, this is important
11 Remove top fork nut
Upside down forks
1 Slide the aluminum top leg until it bottoms out
2 Place fork in spring compressor tool so that the hole on the bottom of the fork leg engages into the tool standoff
3 Adjust tool so that the top threaded studs are lined up with the holes. The spring spacer is located on top of the spring
4 Thread the studs into the spring spacer holes
5 Using tool compress the spring until the dampener rod lock nut is exposed (usually a 14mm wrench can be used)
6 While holding the top fork nut with one wrench loosen the dampener rod lock nut with another wrench
7 Unscrew the fork nut and remove fork nut with attached dampening rod
8 Carefully loosen the spring compressor tool and release the spring tension
9 Remove spring and spring washers
Right side up forks
1 Slide the fork down until it bottoms out
2 While holding the top fork nut with one wrench loosen the dampener rod lock nut with another wrench
3 Unscrew the fork nut and remove fork nut with attached dampening rod
4 Remove spring and spring washers
Draining the oil
Drain the oil by placing the fork upside down over a container. When all of the oil has drained out slide the dampener rod up and down to drain the oil in the cartridge. Do the same with the fork (extend and collapse) until all of the oil is out
Removing and replacing the seal
1 with screwdriver carefully remove dust seal by gently prying around the seal
2 Remove retaining clip that is under the dust seal

3 Remove allen bolt that is located inside the bottom of fork
4 While holding one end of fork slide the other end in the opposite direction until the seal, spacer and top for bearing come out. This step requires numerous extensions as the and seal is a tight fit
5 The seal, spacer and bearing will be on the chromed leg of the fork
6 Remove seal and clean fork leg
7 Tighten the allen bolt removed in step3 to correct torque value
8 Reinstall fork leg into aluminum slider
9 There are special tools for driving the bearing into the slider but a gently used screwdriver and hammer has been effective. I stress the word gently.
10 Once the bearing is seated place the spacer over the bearing
11 Place new seal on fork leg
12 Place old seal over the new seal and using a hammer drive the new seal into the slider. Note: the new seal must be seated full in order for the retaining clip to seat fully
13 Remove old seal and place the dust seal in position
Setting the oil level height
1 Pour oil in until it is approx. 100mm from the top of fork
2 Slide the dampener rod up and down until the fork oil comes through the dampener rod with no bubbles showing
3 Add oil to the level desired. To find oil level go to Race/tech.com. 110 mm is used a lot but check to make sure
Note: To set the correct level take wire coat hanger and bend at your desired level. While putting oil in, stop when oil level reaches the end of your tool. Use a flashlight
Fork assembly
1 Put the spring back into fork
2 Put the washer on top of spring followed by the spacer if any
3 Put washer on top of spacer
4 Make tool with coat hanger (make loop on one end and bend at a 900 angle to snag the dampener rod nut so that the rod can be extended past the spring top)
Pull rod past the top of spring
5 Place slotted washer under dampener rod
Note: Upside down forks need the compressor tool in order to compress the spring. Be careful doing this
7 Install to fork nut and dampener rod
8 Thread the fork nut onto the dampener cartridge rod
9 Screw in the rebound dampener screw and count the turns.
Note: If turns less than desired the fork nut needs to be turned out counter clockwise. If the turns are more than desired turn clockwise
10 when the correct amount of turn are achieved tighten the dampener cartridge rod against the fork nut
Assemble forks on bike in reverse order of disassembly.
Check your maintenance manual for proper torque values
Set your suspension rates accordingly as they have all changed
Clockwise/Anticlockwise – Increase/Decrease Preload, Compression & Rebound Dampening – Harder/Softer suspension

Preload (spring seat) & Sag:
Increase/Decrease – Less/More sag
Each turn = 1 mm preload
Optimum Front Static Sag = 30 mm
Optimum Rear Static Sag = 14 mm