While you have that trans out, do a thorough evaluation of the input shaft bearing. You ran the trans without a pilot bearing for while and may have done some damage to the input bearing, as the tip of the shaft was unsupported. Rather than a shaft that is restrained radially at both ends, you had a shaft hanging in free air. Any imbalance in the clutch assembly would cause radial forces on the input shaft bearing that it normally would not see, as the pilot bearing would limit the amount of deflection.

I had a Honda CRX that I bought used that crunched up an input bearing due to this very problem. When the engine was rebuilt by the previous owners mechanic he forgot to put the pilot bearing back in. Good thing the magnet was right next to the bearing.

Good luck,

Mike