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The 07 pipe is bent slightly different to give additional clearance to get around the 6 speed transmission. That's why you see pipes for touring bikes listed as 97-06 and 07-08.
Ah, didn't think of the tranny be the difference..I have a 6 speed in my 05' which I put in with no probs..was thinking the motors might be slightly different going form a 88 to a 96 and them changing some internals..