Not going in to gear, means your disc is not releasing, i would not think this is trans. related, as it anything was junk in there, you would probably have other issues. Are you adjustments in the clutch correct (the lift the pedal and clicky clicky) The cable is a good spot to start after the adjustments. Also the ATF type, many people complain of crap shifting on different fluids. Im sure you dont want to take that out again.
Also what is your record time to have the trans all the way out. I had 13 hours just to get out. Myself, and in the rust belt (if you could immagine)