generally there is not a lot that gets between the input shaft and the pilot bearing where the input shaft of the trans slides into.
what is happening is, as mentioned, the input shaft of the trans isn't sliding into the pilot bearing. A quick depress of the clutch pedal while your friend bench presses the t5 will release the clutch from the engine, and the t5 is free to slide right in without the clutch pressing against the motor and pp