So if I was running at these speeds and have this issue I should be able to hear the misfire in the exhaust or engine noises right? If I have my windshield all the way up and lean down I can hear a lot better than when I am sitting up, I normally don't do that when I am going that fast since you don't have much time to react to obstacles. I will find a nice quiet strip of road that I can try this on, assuming that I will be able to hear something weird going on. Also, why do I still feel it when I pull the clutch in? Thats the first thing I tried since that would give me somewhere to start, either engine or drive components.
Yeah, if it's still happening with the clutch in, it ain't the motor. Still, you may or may not hear a high speed miss-one cyl dropping quick happens so fast at high r's (at 7000 rpm each cyl fires 3500 times a minute, or about 58 times a second) it's easy to miss it-but still feel it. Doesn't sound like your problem though-and without riding the bike myself, I'm hard pressed to offer much in the way of ideas, just too many possibilities IMHO.