4th gear whines pretty loud

You say used 4 spd OD. Did you go over it before you installed it? I'll bet the PO said it was working fine, no problems. I swapped from auto to manual and the PO owner of the trans said it "worked fine when pulled". Tore it all apart and took all of the internals to Jamie Passon. Some parts were worn specially 2nd gear. Rebuilt it, installed it, and has been working great for well over 2k miles.

Could the 4th gear whine be your rear end? Just a thought.