So you're saying if going 40 mph and you disengage clutch and rev the engine, the vibration is not there? If yes, that to me that points to a mis-aligned clutch disk; or possibly a mis-aligned transmission to bellhousing and/or engine connection.
Worn u-joints will do the same thing. Vibrate under load and not when unloaded (clutch disengaged.) It's easy to check u-joints, which is why I suggested starting there.
