have you checked for the correct insatallation of the pilot bearing. The Pilot bearing centers the input shaft in relation to the crankshaft/flywheel. If the bearing is defective or missing it could cause the input shaft to wobble or be off center. When the cluthch pedal is depressed it frees the driven plate from the pressure plate and might allow it to rattle around. When the pedal is released the plate is clamped down.
Just a thought.