I put a 2" on my 96 600st and didn't have any serious problems with the cables. It's been a while but I'm pretty sure I didn't want to go any further since it was right on the edge of messing with the throttle in tight radius turns. Any input would be helpful from more consistant Yamaha riders.
I believe that as long if you stay with jsut a 2 inch riser it won't mess up anything...I've heard from a sportech racer at the princeton grass drags,(he hated yamaha) he said that with almsot all yamahas that you could only put a 2 inch riser without having to add cable extensions.
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