I had a problem much like that after putting in a new motor. The fingers on the pressure plate had wore uneven and it was a crap shoot every time I pushed in on the clutch. I bet you have a similar issue with things not meshing up right in your clutch. I put in a new clutch, pressure plate, and had it all balanced with the flywheel attached. That was probably overkill but I didn't want to have to do it again. That did fix it.
