If you put the transmission in neutral while driving and let it free-wheel while in neutral will it do the same thing? If so, you can rule out the clutch. If no...that is if this only happens when the clutch is disengaged it could possibly be something with the throwout bearing or something in the transmission. Long shot on the pinion angle I'd think but not an impossible thing. I've had transmission vibrations that vanished when under load and re-appeared when free-wheeling.
