I think you have eliminated it down to something dragging in the clutch. I would try giving the pedal a little less free travel just to try to find the trouble. You shouldn't drive it with no free play, but it will tell you if you are looking in the right direction. Did you remove the transmission from the engine and reinstall it? If so, possibly the pilot bearing got messed up on reinstalling it. Having too much play at the tip of the input shaft will allow the disc to move around.
