I did the same swap on a 1990 4Runner and it was way more work than I first thought it would be. This was a daily driver rig and not a trail rig so a lot of the extra work was making everything look and work as factory.
I had a 1992 4Runner that I bought rolled and was parting out so I had a donor rig to get all the little brackets and trim pieces and stuff I needed. That would be my advise to you is try to find a wreck that you can scavenge everything you will need from. Collecting all the pieces would be a pain.
You need an R150 5 speed to bolt up to the V-6. They have a chain driven transfer case. There are adapters to mate up gear driven cases to them. You won't be able to use the transfer case you have now, and it is a chain type anyway.
Where are you located? I have a complete 5 speed and a complete auto that would work for you. If you are close I will sell them cheap. I don't want to mess with shipping big stuff. I have a few of the install parts if you decide to do the 5 speed swap.
