I knocked this out last weekend. Took about 8 hours but there were a few trips to the parts store.
My notes on top of OP's DIY post:
You need a 30mm socket to get the nut off the output shaft. So if you're planning on doing this get one of those in advance.
If you have aftermarket skids, especially RCI gas tank skid, it'll be A LOT easier if you take it off. Which is a PITA but... it is what it is.
Also, make sure you have plenty of brake clean or other degreaser to clean the oil out of one half of the case. Otherwise, when you go to stab the cases together, the oil runs out and will compromise the effectiveness of your RTV seal. We had to do it twice because we thought we had it clean but oil ran out. I didn't want to find out the hard way that it leaks so we split them again, cleaned the RTV off, cleaned one half of the case (larger half) and re-did those steps.
Another note: If you buy a new motor, that motor will probably be in a different orientation than the one you remove. IDK what the proper method of re-aligning it is, but when I tried to get it out of 4LO (where it was set when we installed it) I ended up hearing a brief grinding noise. And it was only brief because I immediately shifted it into Neutral the moment I heard the sound.
As mentioned in the thread below, I killed my shift motor because mud got into the breather nipple on the motor. Make sure you reconnect the hose.
http://www.toyota-4runner.org/4th-gen-t4rs/206770-save-yourself-$xxxx-your-4x4-zip-tie.html
OP's how to was MASSIVELY helpful. Thank you so much for taking the time to write this up. I litterally printed the entire post and we used it as a guide.