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my 2001 rs after market exhaust can. has had a similar problem.
I went to the dealer for a stepper motor problem ( the bike would idle down and die when I put it 1st gear) while I was at the dealer they put the map in for stock bike with exhaust can. after that I noticed at exacley 4800-5100 rpm the bike was surging kind of like the buffetting you might get being beside a tractor and trailer. It wasn't all the time everytime so it was hard to diagnose. I went back to the dealer and luckily he felt it. He did an ohm test on the something and called his rep , they thought it was probably a TPS throttle position sensor, they did not have one in stock. I thought it was quite a coinsidence that it never did it until the new map, so He put the old, stock map in, and it seem cured, I called back and let him know it must have been the map. He said it can't be the map. well today it started again, so it was not the new map. and like the tech said sometimes the TPS goes out where you ride at and I am at 5000 rpm (80mph alot of the time. so I will have hime send me a new TPS, since they are bolt on non adjusting. something else I noticed today the bike was missing terribly at 5000, while riding I hit the kill switch and restarted it and it seemed to wake up in a different world and rarely did it the rest of the way home.
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