Got the transmission issue figured out. After thinking about it for a couple days and making some phone calls it was a pretty easy decision.
I did the paddle shift project on the auto because it was as close to a manual as I could get at the time and it got me by for years, but it's just not the same as grabbing gears. Now that the auto was failing it was a sign to make the truck the way I always wanted it.
Local salvage yard had a R150F out of a 99 4Runner with 130k on it with transfercase, bell housing, shifters and everything for cheap.
Grabbed a clutch pedal assembly while I was there too.
Drilled through the firewall and mounted the pedal and master cylinder.
Picked up the clutch lines from my local Toyota dealer and found a slave clinder.
Floor cut out and temporary shifter because it's my daily driver.
New clutch kit.
Longer bell housing bolts.
5spd trans mount.
Auto out and put away for another day.
Everything went pretty smooth. Took about 5 hours from start to finish. So much more fun to drive, turbocharger + 5spd = amazing.