I don't think i'd run the 4spd. I would pm malrin and ask him his opinion on that one. You have several tranny choices though. You can run a yota 5spd, preferably an R150 or 151, but some of the others will work. Or you can run a Chevy tranny, 700R4 auto, and adapt it to the yota t-case.
I'm running the R151 that came in my V6 4runner. I'm not a fan of auto's, but it's pretty much personal opion.