hm..i've been dealing with this swap for the past few months so intensely that i can be of help to you. the jdm motor will fit but the wiring harness will not. each coil packs, for instance, have different terminals, so you'd have to buy both the jdm harness and usa harness to get it to fit right. if you are buying an aristo (gs300) clip, you will be need get a new oil pan, the jdm ones wont clear. you may also need new mounts for the motor. jdm motors does not have an egr, which controls smog at cold temps. most supra tt owners block this off anyways, so in a way it's an advantage.
do not attemp going from auto-manual unless you have a lot of money and/or skills at swapping trannies. don't get me wrong, it's totally do-able and have been done, but not easy.
more reasons to get the usdm motor: jdm motors have smaller injectors and smaller turbos. in addition, the turbos are made of ceramic as oppose to the usdm's steal. small fixer upper, but just something good to think about. one site that i found INVALUABLE for this type of information is MKIV.com. definitely check that out.