OK.... So I corrected the start circuit, and grounded pin 50. There was NOT a wire for pin 50 in the plug, so I added one. I took pictures of the location if for some reason there should've already been a wire there.
After about 10 min of driving the CEL came on. Also, the engine died When rolling in nuetral on a freeway offramp, I didn't realize it until I was at the stoplight.
Had the codes read, it was the same P1500 for the cooling fan relay, and P0505 IAC malfunction. Those were the ONLY codes thrown, so I am optimistic about the AT/MT issue. Also, I've never gotten the IAC code before.
I am thinking, disassemble/clean the IAC, reassemble, and see what happens. I'm pretty confident there are no vacuum leaks etc.
Nice. I know I've had to add them before on some later ones, but I thought I'd seen some earlier (96-97) that had the pin. But it sounds like you've got it all sorted out, as far as that's concerned.
Changing the ECU to think it's an MT will change some of the maps for when the IAC opens and such, but AFAIK it doesn't effect how it operates, so it shouldn't require any re-wiring or anything. So yea, clear the code, clean the valve up, and see if it happens again. It may have just been a coincidence.