An easy test for the clutch is to:

Put on the emergency brake.
Put into 1st gear.
Right foot gives gas while the left foot slowly releases the clutch.

If the tach stutters and jumps, there may be a clutch/flywheel issue. If the motor promptly dies, the clutch is probably alright.

There was no rubber left on the driver side motor mount, when I replaced mine. It didn't make any noise though.

Does it make the "clunk" sound if the trans is in neutral when turned off?