...ignition control module on passenger relay bracket...
What is this? The coilpack sits on top of the module.
Could be the module.
Could be a plug wire. How did you test the wires? A visual test doesnt always tell you everything. I have had wires in the past that looked perfect on the outside but when I touched them they were crunchy on the inside like they were burned up under the insulation. Could check the resistance on each with ohm meter. My car would idle fine and drive okay until I tried to get into it. Car would backfire when I got on it.
Ohming out the coilpack across the towers is always the first thing you do when it is suspect. Should be 11k-13k. If there is a problem with the coil you will usually see it here. The module is another story.
The Temp idiot light is connected to the temp switch. Is that what you shorted out? Just want to verify because you mentioned the temp sensor which if that is bad WILL give you problems for sure. Do your temp readings read correctly with a scantool?
Also check your voltage. Could be an alternator issue. Check both at idle and under load.
One badly gapped plug wont do it. If all the plugs arent gapped correctly then might. I know a guy who changed his plugs and obviously didnt know what he was doing. He had them all gapped at over 60+ if I recall. Car did not like it at all.
What are your BLM #s?
Any VAC leaks or exhaust leaks?
Any ECM malf codes?
What condition is the O2 sensor? Do O2 cross counts move okay?
Cat or no Cat? What condition?
IAC #s?
Verify that TB blade is opening all the way.
Swapping in a known good MAF sensor wouldnt hurt to help the process of elimination. Try the tap test with scew driver or something and see if the car stumbles.
Make sure TPS is #s look okay and are not jumping around while driving, etc.