My two cents,
for anyone who's still following this thread, I had the exact same problem the original poster experienced, I couldn't completely seat the Transmission up against the engine, I was falling short about 1 inch, the dowel pins where just barely making contact with bell housing. So after around 8 hours of trying to force it in, I dropped the whole trans together and took a better look at the TC, sure enough I wiggled and pushed it and it went in a little further and then wiggled it in more as Im turning the tc both clockwise and counter clockwise and it went in a little further until it bottomed out against the bellhousing. Didn't realize just how far it had to go, surprisingly even after all the mule kicks, I didnt ruin my TC. Thank God!