It is FINISHED.
I actually got it done the other day, but wanted to test drive her a few times in case something went wrong and I had to do it all over again.
Nothing did though, and I now have a 5 speed! Redline MT90 in both transfer case and tranny. Shifts great even though I'm not very good at driving a stick yet.
While I was in there I ended up replacing 4 of my lifters on the passenger side - which completely got rid of my lifter tick, I replaced all the screws for the head covers with bolts, replaced the leaking bypass hose - which has completely solved my overheating issue, and did the mean grean alt install, and mounted the taurus fan properly (no more plastic mount things).
Just a couple of loose ends left to tie off: need some new breather hose for the tranny as the old one cracked apart, need to mount the clutch floor stop bracket so I dont push it all the way to the firewall when shifting, then need to run the interlock lines to a switch on this JIC someone were to try to start the truck without depressing the clutch (might run a kill switch on the dash too), and need to replace the BRAND NEW clutch slave cylinder as the bleed screw broke off when I tried to tighten it.
Oh, and of course re-do the UCA's (again...will be my 3rd time changing them haha) and get an alignment.
I couldn't have done it without all you guys. Special thanks go out to Sammyb33, unccpathfinder, and especially KovemaN who helped me pull the JY tranny and the dead auto tranny.
Write up with pics soon to come.