You aren't really specific about your problems with the shift linkage but I did have a problem. and it's documented in my old thread.
When I mocked everything up and measured the shift rod, it appeared as if the only trans lever I could use was one from a GS and that particular one angles pretty far forward. Unfortunately, that set-up didn't work very well.
Luckily, inmate Max Headroom suggested that I try a different shifter and one from an RS looked to have a better angle. After measuring again, chopping off the end of the linkage and rethreading it, all has been well with the world but I'm still thinking about the rear brake situation.
Ok... I went and looked at your photos and yes , my shift rod was a little long as was yours. You asked for a new part and I fixed the part I had on hand.
Now. About moving those peg mounting holes! If you look at the back side of that bracket you'll see that it's reinforced using what appears to be a HD washer. IMO, that reinforcement needs to be augmented but you may well have drilled a hole that bypasses the reinforcement entirely. You really don't want that right peg to bend while you're hanging off in a fast, tight, right turn do you? (Correct answer = "No!") . Just make sure your installation is solid, stable and safe.
Other than that, ride fast and take chances!
Hate rots the pocket that carries it.
Hawk Medicine screwed with this post 03-21-2011 at 12:57 AM