Would the clutch know it was under a load? I can see where it would vibrate with clutch disengaged, but why under a load? Could the engine be lean and running rough and not really a vibration? I would think something would have to be pretty bad to vibrate a 500 rpm (idle). Is the harmonic balancer straight? What does it do at idle with the clutch in then out? did it change? How do you feel the vibration, in the steering wheel, the floor, seat of pants, clutch lever? Could be pushing the clutch in rock the motor or put strain on the mounts? Is the exhaust pipe rubbing? What about high rpm sitting still? does it get worse going through a certain rpm range? can you hold at a givin point to make it vibrate?
This is a strange problem, I just threw this stuff out. It may all be trash, just stuff I thought of. Keep us posted, Joe