Well, What I'm understanding here is that the OP re-wired the car, and now somehow the HAC sensor is not working.
From this, I deduce that the OP HAS a HAC sensor, so it's an '86.5-'88 car. I also deduce that there's a code coming up in the ECU and that it's probably a HAC sensor code, causing the ECU to go into a limp mode all the time (Or just light the CEL), even though there shouldn't be a high altitude to compensate for.
What I'd suggest is that you fix the wiring. It's a couple of short wires to the HAC sensor, and one connector. It shouldn't be THAT much of a problem to figure out what happened to it.
If the ECU is a newer one ('89+ car) then a HAC sensor code means that you did something bad to the ECU and you should replace it. I suppose that's a possibility for the older ECU as well, which I'd confirm by checking/testing the HAC sensor wiring. Really, it's one of the shortest wire runs int he entire car, how hard can it be to troubleshoot?