I had the same problem with that wire not long after I got my '03. It broke into literally a million pieces, most of which were caught by the strainer but nevertheless I still had to strip the entire motor and remove all the bits. It put a mark on the crank's primary gear which meshes with the clutch basket but at least 15k miles on, no problems. Open that strainer up (quite easy to work out how to) as you'll never clean it out completely closed. I do this with every engine I strip. They go back together easily and securely afterwards with care.
Like Long has said, it'll be the dogs on the gears which are worn, not normally the teeth. I've done loads of R1's now. Remember to replace all corresponding gears that mesh their dogs with worn dogs on other gears. New ones meshing on worn will accelerate wear very quickly. Basically, spot one worn gear, replace everyone in that 'chain'. You'll regret it if you don't in the long run.
For most 2nd gear problems you need to replace gear-wise:
Gear, 4th wheel
Gear, 2nd wheel
Gear, 6th wheel
Plus any other parts worn/damaged. It's normally Fork, shift 1 which suffers the most.
Check shift forks for straightness/wear too and the shafts they run on should be replaced also. They almost always have some degree of bend to them which if used again like that will just bend another new shift fork quickly. They're not much money at all
Oh, and leave that wire out, doesn't do a damn thing in my experience... It's supposed to make the clutch quieter but I'll bet you notice no difference at all :fact
