Unless you find out its in your harness, which I don't see happening but maybe(not ruling that out completely), if your breaking up in the top end RPMs its possible that its detonating and not getting enough fuel, to much timing, too much compression and timing together etc etc.
Ive actually had this happen to me once, all I did was change domes and la la, my bike started breaking up in the top end. Not long after that it was motor rebuild time lol, not kidding. It could be just a pipe change, dome change, timing change, blah blah. Its just enough to cause your motor to detonate before it should.