The smoking gun here is....... it was shifting before you took it apart and it’s not shifting after you put it back together. There is no easy fix. You are going to have to pull it back apart at least as far as your original disassembly. Get a copy of the FAM for your particular truck and reassemble very carefully. Good luck.
You are definitely correct. Something doesn't seem to have went back together correctly, I've had the thing off now a half a dozen times and still haven't been able to figure it out. I have an assembly manual (not the easiest thing to figure out which application goes with which), but I will try again....what choice have I got?