You posted this in the FAQ section. That's essentially a reference area and not for general discussion. I've moved it to the main MKIII section where it belongs.
Haynes is a poor reference for most vehicles and the Supra isn't an exception. Return it and purchase Toyota's Service manuals... You'll be glad you did in the end. They're worth every penny of the MSRP but if you can get them used well, all the better. Here's an online version for the '90 Supra, both TSRM and TEWD (that's Toyota Service and Repair Manual and Toyota Electrical and Wiring Diagrams):
http://www.cygnusx1.net/Supra/Library/TSRM/MK3/
http://www.cygnusx1.net/Supra/Library/TEWD/MK3/
The alarm system will not disable the radio in stock form so no worries there... :P In my post in the FAQ section I've covered what has to be done to reset and/or delete the factory alarm system. Read it and reverse it if you want to enable the system. You'll most likely need to replace the lock switches in the doors though. Personally, I'd replace it with a modern alarm.