You've left out an important piece of information; Just how much experience do you have with automotive repair? The only advice I have to offer to a complete novice who's looking to do their first swap is to find a local MKIII owner who has experience with the project and is willing to mentor you. IMHO, it's not the kind of thing which can be talked through over the net with most people.
I STRONGLY recommend you go to a Toyota dealership and buy or order online a copy of the Toyota Service and Repair Manual for 1987 Supra. It is more accurate and specific than other third-party manuals and will walk you through the complete rebuild process. (It also makes for a badass booster seat! The thing's a damned phone book.)
Here you'll find an online copy of the TSRM for a 1990 Supra:
http://www.cygnusx1.net/Supra/Library/TSRM/MK3/
Are you planning on a GE to GTE swap? Your profile (and signature) has no information for us to know what you've got... hint.