I've been here before. I spent 3 weeks of my time checking everything, from the all the wires on the ECU for ignition, to the main relay, to the ignition switch, to the ignition control module, and everything in between. I traced all the wiring for the entire ignition system. I couldn't find the problem. I replaced the ECU and the ICM. Didn't help.
I finally found it, and I should have known the whole time. I had a bad ground (The ground that was on the fuel rail on the passenger side). I checked that the first day when I checked the voltage on the ignition control module, but I was checking for voltage and when the ground had none I said "Well that's normal" and moved on. I didn't check for a grounded connection like I should have.