Plenty of people swapped out the stock 5 speed for automatics. I will be swaping out mine to once it goes! Use the search buttom and you will find a lot of information about it. TH400 is a popular tranny that will hold some HP. You will need adapater plates and a few other parts..
ANY built stock yota autos will break after 500 rwhp...especially if you drag race the car or use any kind of slicks. 2nd gear is really weak, and no company does anything to address this weakness. so stay away from those. 6 sp would be the most enjoyable to drive in my opinion. im sure some people have gone from 5 sp to th400...i know people who have gone 6 sp to th400.
the TH400 is really the only option for a good built auto. and it is way cheaper than swapping a 6 speed, however if you are already 5 sp it may be more enjoyable to have the 6 sp.
a built th400 is around $450-650, and the flexplate/adapter plate cost around $1000-1500. in addition you'll need to cut the drive shaft, make a custom adapter from the shaft to the rear diff, and fab some tranny mounts. when you install it you gotta hammer out you tranny tunnel to fit with some kits. others like SP's are a direct bolt up and no hammering needed, but a little more spendy.
if you switch from your 5 sp to the 6 sp it should cost $2500 for a used tranny or around $4500 for a new one depending if you use v160 or v161. i think youll need a new clutch, new driveshaft, and possibly a new flywheel. (im not sure if the 5sp uses the same flywheel as the 6sp.) and you may also need tranny mounts and a new rear end assy., axles pumpkin etc. to change out to a full 6 sp setup, you dont want to use that stock lsd or non lsd rear.
the th400 saps around 100 rwhp, but actually increases your 1/4 mile times over 6 sp (typically). so a car that puts 650 hp to the wheels through a 6 sp will put down a little over 550 with a th400, however the th400 equipped car will have better 1/4 mile times (depeding on the driver and quality of build). so its really what you want out of the car and how you drive. also you can get gearvendors over drive kits for the th400 for around $2500-4500, that will take it from 3 gears to as many as 6 gears, and you can even pick some of the gear ratios. thats a cool option, takes it form being limited as a drag car to just about any kind of racing you want. thats another prob with the th400...youll run around 3650 rpm just to go 65 mph.
im putting a th400 into my SC300 so ive been researching all this stuff quite a bit and talked to a lot of shops about it. im having a tranny built already, to handle 800rwhp. i havent picked it up yet tho as im kinda lazy, and the car doesnt even run yet. im waiting to get aem and some other mods to do the th400 as well. anyways hope this helps thats all i know about tranny swaps into NAs.
Thanks to both of you especially eblick99 that was very helpful and exactly the answer I was looking for. I'm in the process of getting a supra so just wanted to know my options before I got the vehicle.