Victory! Got everything reinstalled besides the skids and grille, took it for a test drive, fine tuned the fluid levels, etc. Everything is functioning nicely, the transmission seems to shift perfectly. In subfreezing temps with the aux cooler I had to simulate some towing with a little brake pedal to get it up to specified operating temperature, but everything went pretty smoothly. No leaks so far but I plan to run skidless for a bit to closely monitor everything for leaks and fluid levels.
Here's how I ended up running the cooler hoses, I pulled the airbox and put in another hole to avoid anything remotely resembling a kink:
The plumbing I chose to go with is trans send line -> close radiator port ->far radiator port -> lower aux cooler port -> upper aux cooler port -> trans receive line. I figure (and Hayden manual agrees) this will give the maximum cooling, but may cause me to run a little cool in the cold.
I bought another cheap bluetooth OBDII reader to leave permanently connected to monitor trans temps on my android head unit:
Tim was pretty much spot on with the fill procedure and volumes. I started with 4 quarts and ran it for a second. That wasn't enough to move much fluid so i ran it for a little longer. Then I added 2 more quarts, ran it for a few seconds, added 2 more after checking the level, then added 1 more, 1 more and about a half more. I ended up at about 10.5 quarts in before my test drive which was just below the cold level on the dipstick. After getting it up to operating temperature added about 1.25 more to get it to the upper end of the hot range. I used about 8ft of 3/8 hose (started with 2x 5ft kits). I will be monitoring this closely over the next few weeks.
While still fresh here are some tools I found handy to have:
wobble extensions, lisle funnel for coolant fill, flex ratcheting boxed wrenches, ujoint sockets, medium quality trans jack or better, a strong friend to lift steel bumpers/transmission and spot the transfer case, and a thread chaser kit. If i did it again i would take great care to clean/reform any aluminum threads. I'll post more stuff as i think of it.
Here's my finalish part list:
Transmission
90301-09011 Automatic Transmission Dipstick Tube O-Ring
Hayden 699 and a way to mount it
3/8" Transmission Cooler Hose
Heater hose or something for hose abrasion protection
12qt Valvoline Max Life Synthetic
33555-35160 BOOT, SHIFT LEVER (only if damaged)
12371-62120 INSULATOR, ENGINE MO (transmission mount only if damaged or makes you feel good)
Starter (only if you feel like it, mine was pretty worn and dirty at 211k. My previous 2 3rd gens had starter issues eventually so not a bad idea)
28226-54340 STARTER KIT, BATTERY TERMINAL
28226-72010 STARTER KIT, MOTOR TERMINAL
28235-54380 PLUNGER, MAGNET SWITCH
28175-54380 GASKET; PACKING (might be able to reuse but FSM says single use)
2x 28199-74110 PRORECTER, DUST STAR (I broke my vents off in removal but they were quite brittle anyways)
2x 90099-14064 O-Ring (If you disassemble the motor side. I haven't heard of many failures but mine was very dirty and could use some grease)
Engine
90311-A0027 Engine Crankshaft Seal (Rear main seal, if you feel like it. Requires red loctite/TB1324)
Blue loctite for flexplate to torque converter (not specified in FSM but seems like a good idea)
16410-AZ011 Radiator Assembly
90480-25025 GROMMET coolant resevoir tank (you probably don't need it but i took my resevoir out, cleaned it, and the grommet at the bottom was missing somehow)
2gal Toyota long life coolant
2gal distilled water
I had recently replaced my radiator cap but that might be a good idea if you haven't.
I'll edit this post if I recall anything I missed.
I considered extending the breathers on the trans and transfer case, but decided against it out of fear of affecting my warranty. If i went with a used trans I would have done so while everything was out. There is a decent thread or two on here about it.
I still need to return the incorrect pan to Yota1 and look into my core charge. They said they were going to send me a return shipping label for the pan but I don't believe I've received one so I'll have to chase that down. Once my business with them is settled I'll write something of a review on them and a summary of my experience- it seems there's a decent amount of interest in that aspect of my adventure.
Thanks again everyone for the moral and technical support. This was my biggest auto job by a decent margin so far and it feels good man. Happy to answer any questions anyone may have.
if your super concerned about it put a little blue loctite on it. 
