Reading the posts carefully I see a couple strong clues that the vibrations are due to a chassis/ frame resonance.
First: yamadoc wrote "Strange thing.. the motor itself has very LITTLE vibration.. but the oil tank, frame, handle bars, and seat really rock...weird "
Second: DYNAREX wrote " hey yamadoc ive got the same vibration in mine-
ive tried with the clutch off-feel it about 4000 then 6000 then at 8000 rpms "
Both are exactly the way a chassis resonance would act.
Since in both cases it was not there initially, Look for somthing loose or broken. Engine mounts, suspension bolts. It still may be due to an engine problem but at this point I doubt it.
To understand the resonance phenomenon. If you bolted one end a hack saw blade to the engine you would see that at certain rpms the blade would vibrate wildly. ( no need to do this but visualize)
There may be something in common to the problem joe howard and I have.