Help, what the heck have I done?

I'd reassemble it as is. First, confirm the rotor spacing right to left. Both sides should be reasonably equal. See if it touches when you spin the wheel, since it's buffed down it may not but you can flex the rotor enough by hand to see if it is very close. Again, compare side to side.

Lastly, pull the brake lever and see if the rotor pulls over.

If it's close in general, you have a spacing/bearing issue. If it pulls over with brake pressure you have a stuck piston/ but as even as the pads are I'd doubt a stuck piston. One would have them all a little different, two is unlikely to stick at the same time. I haven't had the brakes on a Gen 2 apart but a possibility is that when you mounted your last tires the caliper was crooked/shifted over when you tightened it up. If it can move side to side an appreciable amount that could be all it is, just enough difference to make contact.
 
When I figure it out, it's probably gonna be an epic DUH moment....:laugh:
 
If I remember right, there is no spacer on the left side and the axle has a step up or shoulder on that side that acts like the spacer and rides on in the seal on that side. You said the axle part #'s are different so that might be the problem. Maybe the step up shoulder on that axle is a different length and is letting the wheel slide to the left too far. Put the Busa axle and the Gixxer axle side by side and compare.
 
I haven't seen this thread til now but I was definitely baffled when Keith called me and sent me pictures. It's definitely not missing any hardware or spacers. There is only one spacer and it's on the right hand side of the wheel. I actually called Keith back before I left work and I told him the only thing I could come up with was that he somehow compressed the pistons in to far at one point and caused the piston to get stuck on one of the seals in the caliper.

There is really nothing to the front wheel as far as hardware is concerned to screw up a front wheel removal/install
 
had the same problem with a bike I once had the pistons are stuck a rebuild kit solves the problem. Its as simple as that.
 
Ok, here's the update:

My neighbor brought his 08 Blue over last night (he finally did join, but only lurks and couldn't remember his username - so THANKS DAN!). I took off his front wheel, and compared parts. The spacer and axle were identical (so no I hadn't swapped any parts by mistake). I measured the distance between the forks (also identical, so forks were not bent). Then, I measured the distance from the outside of one disc, to the outside of the other - and mine were 1/16 of an inch LARGER than his. So, I mounted my wheel on his bike, with his parts. When we put the calipers on, the right side fit perfect, but the left side did not; the caliper was off by about 1/16 of an inch for the caliper to mate to its other half on the left side fork tube (which means ours matched perfectly on the right side, but the difference in the spacing is on the left side (where the caliper was messed up) (first pic below). When I moved the pads a little to get the caliper on and looked, it repeated the same problem I had on my bike (where the pad/disc was almost touching the inside of the caliper. After spinning the wheel a little and watching, Dan said "see, watch the disc as it rotates, it's warped" and when I put my reading glasses on :banghead:, he was right. The left disc is NOT straight.

Caliper: I blocked all the other pistons on both calipers, and pumped the brakes. The pistons on the faulty caliper came out, but what was interesting is that they were spotless, clean from the last time I changed pads (second pic below). That tells me that the pistons had not extended at all since the last time I cleaned them. They did not leak, so no seals are busted, although they may have locked just enough that there wasn't enough pressure to extend/even them with the other side. I will be carefully cleaning them again tonight. It is entirely possible that I pushed them in too far when I put the new pads on, and they got locked down on one side. I can see how the piston might need to be partially extended to make is start working right, as it would require more pressure to move a fully closed piston than a partially extended one (fluid dynamics).

SO, the question becomes, did the warped disc cause the caliper piston problem, or did the caliper piston problem warp/bend the disc? I don't think I'll know until I put a new disc on, and clean the caliper, put it all back together and see how it fits.

Twobrothers has graciously offered to overnight me both his rotors, and I am going to try either/both of them and see what happens. If that corrects the problem, I'll probably order a set of Galfer discs and give Charlie his back when they arrive/install. At least this way I'll be good for the bash :please:

Thank you all for your insight.

P.S. Earlybird - It WAS the fuel pump!

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I have two lessons learned:

1. Be careful/guard the rotors when you have it off the bike, as they may be more delicate than you think.

2. Never FULLY close the pistons when putting new pads on, and Visually check that the both come back out after you put your bike back together and ride it. Because the brakes seemed to work fine when I bedded the pads in, I did not got back and visually check that both sides of the pads had actually floated/centered...
 
Glad to help you out anytime Keith! Hope you got your problems straight on both bike and truck!
 
I bet that the pistons/pad warped the rotor after being compressed too far during a pad change. I learned that lesson many years ago when I did the same thing to a car. I never push the pistons down all the way, and always clean them before compressing during a pad change.
 
Excellent source of knowledge here good words of wisdom to all of us who work on our own bikes.
general summary:

1. don't over compress pistons
2. rotors are more delicate then you think
3. pump brakes after the job is finished
4. go back and inspect for piston movement in all calibers.
 
Twobrothers sent me his rotors should be here today, but I might not be able to try one out until Monday :(
 
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