... and I thought I would see what happens when the clutch is pulled in at about 45 miles per hour...what do you know? The vibration disappeared. This tells me that the tires or rims are not to blame. Right?
Probably, but not necessarily. When you pull the clutch you also take away the tension from the chain and from the rear hub. Check that there is no freeplay in the rear swingarm, wheel and hub. If it's all tight I guess it most be an engine problem.
Oh, one more thing. I had this annoying vibration thing for almost a year. I check all motor bolts again and again. But on close inspection i found that one of the mounts had a fine line in it. When I removed the bolt, the mount fell off! After welding it back on vibrations were all gone.