[joeswamp]

Maybe I'm being thick here, but how would a clogged pilot jet cause this problem? I thought the pilot jet just allowed the engine to idle, once you're above 3-4k rpm or so it becomes kind of irrelevant. I thought the symptom of a clogged pilot jet was that the bike was hard to start without ether and hard to keep it running below a certain rpm.

This sounds like a clogged or messed up petcock and/or or venting issue to me, like maybe your petcock is flowing enough fuel to run normally but not enough to run at race pace. Are you sure it's a fuel issue? Could it be an overheating coil or something?