The one red wire goes directly from the starter to the ignition switch through a fuseable link. I agree that one wire goes to the HVAC system and one wire goes to the alternator, it also splits at S201 and goes throught the fuseblock (C100) to the ignition switch. I guess you could also check at the connector behind the passenger side valve cover to help narrow down the problem to see if there is 12V there.
Ive had the experience of having a bad ignition switch in one G body and a bad fuseable link in another, but since the OP has modified his car anything is possible.
Best thing I have ever learned about diagnosing cars is to break the larger problems into smaller parts, for example on the OPs problem, start by is it a problem under the hood or under the dash.
