Today has been a bit frustrating.. but it's alright - this is a learning process.
Woke up early and got the flywheel and clutch kit torqued down, replaced the throw out bearing, and started mating the transmission up to the motor, where I ran into problem 1.
Problem 1: The little guide posts that come out of the bell housing of the transmission - one of them was running straight into another guide post on the motor, so since they are just pressed in, I pulled one out with vice grips and continued on, but it halted my progress for a bit.
Problem 2: I knew going into this that the bolt holes on the transmission didn't match perfectly to the 1MZ... but I was only able to get the two big bolts on top of the transmission in. I then found another matching one towards the bottom of the transmission. The last (4th) bolt that lines up isn't actually a bolt hole at all - it's a spot for a guide post thing to into the engine. No problem - I'll tap it. This leads me to problem number 3.
Problem 3: I live about 15 minutes away from the nearest town. I don't have the luxury of just heading into town for this or that. So I went into town to get a tap for the bolt hole. It was confirmed by V6 guru Jim King on MR2OC that the hole needs to be drilled and tapped for 12x1.25, which is what the main transmission bolts are. I went to town to get one, walked into the hardware store, grabbed the tap, paid and walked out. I got all the way home and started tapping the hole when I realized it wasn't working. I glanced at the package and realized I bought a 10x1.25, not a 12x1.25... And at that point I said screw it - I'm done for the day. I'm not driving all the way back to town for that. Not today.
So I'm stopped until I get home from work tomorrow. I'll go snap some pictures for you guys right now, but I can assure you they're a bit disappointing in terms of progress. I'm personally really peeved on how little I got done this weekend.

On the other hand it's alright, because my new kirkosaurus mounts aren't here yet, nor are my shift cable bushings from CRW, and my DGR coilovers. They'll all be here tomorrow, so I would have needed to revisit a few things if I were to have installed it already.