Argh, sorry to hear about your wiring nightmare. I'd take it to someone who can sort out the mess, I'm sure someone on here will help you. Make sure that the pinout is correct on your ECU connectors also, the PR3 pinout is not the same as the pinout for the HF ECU that came in the car. I don't play with OBD0 stuff really so I can't help you much. I'm guessing you have a bad connection somewhere or that something just isn't complete all the way.
People like to drop another engine in and then butcher the wiring really bad, I've seen it so many times. I'm an electronics technician and it makes me sad to see people ruin a perfectly good harness when they don't know what they're doing.