I was asked if I had any thoughts or tips on the R&R, thought I would post here too...
Things I would do differently or just thoughts in general...
Clean everything as much as possible before you dig in. Oil, grease, dirt, etc. just make it all a more miserable job. I never planned to tear in to this thing like i did, so I didn't clean it well before starting. Degrease, pressure wash, etc.
The HF 800 pound lift is great, and worked fine even on 35's, but the transmission with transfer case seems maybe too heavy for it, and I couldn't find a balance point for the combo on the platform. I took them out together, with the tranny jack under the tranny pan and a floor jack under the transfer case. Putting the transmission back in alone was a breeze with the tranny jack and with it and the truck cleaned up.
Remove the transmission and transfer case shifters completely before even trying to drop the transmission. It's tempting to leave the transfer case shifter, don't. It really needs to come off to pull the transmission far enough back to remove. Also, with both of those removed, you have fair access to the top two bellhousing to engine bolts after lowering the back of the transmission. They are a PITA still, but a couple feet of extensions does it, as opposed to trying to get to them from under the truck, behind the transmission. I also used my cell phone camera to watch while I snuck up on the bolts with the socket. the valley in the bellhousing around the bolt heads provides a bit of a guide.
Make sure the fan / radiator don't make contact when lowering the back of the transmission, loosen the fan shroud and put a block under the oil pan on a jack stand or on the cross bar to make sure the engine can't tilt too far forward once the transmission is out. Mine seemed fairly well balanced on the engine mounts held in place by the exhaust. I do have brand new engine mounts too. IDK, the FSM says do it, I did it.
Don't forget the cooler line mounts at the bellhousing and above the adapters on the right side.
Be very careful when lowering. It will be a pain in the ass to stop, get up, walk around, etc., but make sure the wiring harness doesn't catch on the cooler lines. Mine did, and damaged a couple (new) connectors.
Don't go all OCD and clean all the years worth of gunk under there while you are in there. It's pretty, but it cost me weeks and made me lose interest in the truck for the first time ever. Or do, it that makes you happy. Do handle anything that really does make sense to do while you are in there.
With the transfer case out, it is a good time to go ahead and open it up for new gears, bearings and seals...
Edit, I almost forgot, because I ran in to this before pulling the transmission, but go through the harness while you are in there. My transmission harness was in far worse shape than my engine harness. Clean, re-loom, replace any broken connectors (almost all housings are still available from Toyota). No D light, or PRNDL at all ? Now's your chance.
Jason