Originally Posted by Northern Dog
I'm gonna throw in my 2¢ worth at this point ...
I've seen problems in the past on bikes and cars where the ignition/spark would break down once you reached a certain rpm range. Have you tried swapping out the coil and/or CDI yet? ... it also may be something as simple as a faulty plug wire/cap.
It could also be as simple as a loose connection. I had a loose coil wire cause me grief with my 600 and it was dependent on rpm and not throttle input. The plug was also black regardless of jetting which made me start suspecting ignition. Pinched the connection down tight and it ran great.