To keep things in this list instead of just in the "what'd you do today" thread I bashed the thing back together last weekend... Friday I got both transmissions torn apart and Saturday I got to swapping parts around onto the new output shaft. For the most part that went all fine until I realized I didn't have any super strong loctite for the counter shaft races (for good measure, don't need them to have any excuse not to spin). By the end of the day I had everything sealed up and assembled ready to be put in Sunday which worked fine, the throwout bearing I put in last time squealed from the start so I put the one that was on the donor trans and that worked out great.
After I got the trans and drivetrain in I moved to the front brakes, changed the one rotor that I knew was bad and new pads of course then moved to the other side and found a cracked rotor and a sticky caliper so changed that and the other rotor (bought rotors at Advance when they were closing conveniently, didn't have any calipers or pads though...).
First test drive was before bleeding the brakes (gravity bleeding wasn't working and the wife was out shopping) and the only complaint is it doesn't stay in reverse... which is still the case but I met the deadline I set for myself and it works. Judging by the videos on YouTube when I was making sure I was putting the transmission together right there's like 5 videos about not staying in reverse so I'll look into that... will try my second shift tower first since it's the easiest though.
I think it drives better than it has since I've had the thing... clutch chatter and squeal is gone, everything actually worked out... so far.
Oh and when I was getting ready to back it out of the shop I noticed a tire was low then saw the rock in the center of the tread... the tires are like 11 years old so even if it wasn't Sunday evening a shop likely wouldn't have done anything to it so I pulled the tire, broke the beads free and put a plug/patch in there, worked out but those Goodyear Duratrac tires have some mean beads... when it gets time to get new tires I think I'll stick with those... I have around 35k miles of just towing miles on them and they've held up great.