Well, if the engine vibrates with the clutch pedal pushed in, then the vibration is coming from your engine. With the pedal pushed in, the clutch is NOT ENGAGED!
The flywheel/pressure plate are the only things that still spin when the clutch pedal is pushed in.
Both the pressure plate and the flywheel have the 50oz imbalance to them. Meaning if you install the pressure plate or flywheel 180 degrees from where it was before, vibrations will occur.
It's the same as the driveshaft. The driveshaft is EXTERNALLY balanced, with weights on one side. Turning it 180 degrees will get the same vibrations. But since you get the vibrations with the pedal pushed in, it has to be the pressure plate/flywheel.
Scott