I apologize if I missed this or not, I just skimmed through this thread - did you look further into the possibility of some binding at the crank? Was the crank originally drilled for a manual tranny? I think I read that you installed the roller-type pilot bearing, but don;t you sometimes have to trim the end of the input shaft for clearance issues? Maybe the end of the shaft is making contact with the crank and that's the squeaking and binding you are experiencing.
I think that issue would display all the symptoms you are describing.
