I've rebuilt quite a few Toyota manuals. They are super easy. Pull the front bearing retainer on the input shaft, and unbolt the center 'plate' from the case to see what you are looking at. Its been a few years, but it seems like I was buying rebuild kits with Koyo bearings through the gear supplier to my Chevy dealership for about $100. If there were hard parts that were bad, like a shaft or gear, it cost a little more.
I also have a tranny and t-case in the garage from an 88 4runner, not sure which one it is, I'd have to look.