John,
It sounds like you're going through what I went through when I first got my 88. Someone's hands had been all in it that didn't know what they were doing. It had been converted to mass air and when I tried to pull the codes, I had to do some crazy stuff just to get the code reader to pull anything. I had to connect one wire to the positive side of the battery, then another to the EEC ground, or something like that (sorry it's been a while). Then it would pull like 12 codes. I replaced the EEC, and that fixed part of my problems, but not all of them. Anyways the best thing that I can suggest you do is grab a haynes manual for your car and pull the passenger side kick panel off and start referencing wires. Make sure they're where they need to be especially for the MAF. There are 4 wires from the MAF that SOMEBODY obviously put in there, or at least attempted to. Make sure the wiring diagram matches up with your wiring. Then if you still have problems, try and borrow a friend's EEC out of another 89-93, and see if that makes a difference. If you don't already have one, then go get a code scanner from the parts store for about $35.
Dave
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