I contribute your problem to the flywheel not being resurfaced. Simple as that. You are not going to see or feel with your hand the SLIGHTEST imperfections in your flywheel. But you sure will feel it through the clutch pedal. Just like brakes. But who cares, you said you're taking it apart again anyway. Now you know, that the only way to be certain you won't have the problem in the future is to resurface the flywheel and get a matching clutchdisk and pressure plate. Simple as that.
