Here is a vid of my Trooper exhibiting it's tranny noise:
After taking some opinions, I decided to swap the tranny. Most likely the bearings in the transfer case. I don't know much about the inner workings of transmissions though. Swap is much cheaper and easier than a rebuild, I bought a whole parts Trooper for $100. So, here comes the replacement ferried by my dad's Tacoma.
My clutch was trashed, possibly because I slipped it being far too aggressive during break in and/or I torqued it down with the clutch disc in backwards on my first installation attempt (it didn't work like that). So, I special ordered a Centerforce Dual-Friction clutch. They don't stock that part # anymore, so I had to be made to order. I don't know of any other performance clutches for this application (91-92 Isuzu Rodeo w/ 3.1L, 9-5/8" disc). My truck is actually a '90 Trooper with a 3.4L swapped in place of the original 2.8L (normally equipped with a 9-1/8" disc, that's the size I ate up, but a from a cheap set - not a centerforce).
The engine stayed pretty well on it's own, but I had the hoist on there for good measure.
The project was a success. I'm back on the road with no odd noises and a properly working clutch, which I plan to break in very gently and properly.
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