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These are just ideas, but not seeing the car first hand makes it difficult. You'll have to go through a Process of Elimination to try and determine what circuits are whacky, and if their is any relationship between them, that is .....do they share the same power feed.... or ground? Have you checked and cleaned all of your grounds carefully? If you are confident you got the wires back in the pigtails correctly (which sounds like you were cautious) then I would try to check the PCM as stated earlier. I went through mine with a digital volt meter and checked the connectors that plug into the PCM to see if they were running at the proper voltages, the PCM is also grounded independently to the car body under the dash (check that one too). I resolved alot of weird signals on mine by cleaning the contacts on the "All" fuses (w/pencil eraser), sounds strange but I noticed they looked discolored from heat (which was created from resistance -poor continuity) Actually eliminated a few minor problems. Last resort, instead of getting a new PCM, and re-using the PROM chip that "could" have a problem, I would try to locate another chip, or a box (PCM) with a chip in it already (number matching your chip), and swap them real quick to see if any changes are noticed. Do you know anyone at all that has model year same as yours that is working good, and could swap out the PCM temporalily? I wouldnt want to spend $$$ on a new one unless absolutely necessary.
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