Before I drop 100+ on a battery: I have been driving with a meter in the car. So I test voltage like when I get to work. The battery is giving me 12.8 to 13 V. when the car is off. And like 15V when its running. These #'* seem a bit high, but I can't see either being a misfire cause. I think I will try the TPS and go from there.
IF I decide to replace the ECM, I see some of these say they need to be programmed. Is this accurate?

I would like to know what the current obd codes are again.
Clear the codes by removing both battery terminals for 5 minutes, then restart the car and take it for a drive.
Test for the codes again since the SES light does come and go. Post back the code numbers ie- #15
Here is a video that may be helpful....

Actually, the car went into extra crap mode. So the SES hasn't gone out in days. But, I will reference the video. Maybe see something the charts didn't show. Battery is already disco'd for reset. So will report findings.

I have to ask this before I go too far. Does my 93 88 have both an upper and lower coolant temp sensor? The parts stores by me are baffled. If it does, where the heck is the lower one?

Wish I could help but I dont have a FSM for your 93/88
I am hopeful another member may chime in to help on the coolant sensors question.
Hang in there..

I was thinking it was 1 sensor with 2 elements, one that feeds the gauge, the other the PCM. I don't remember seeing one in my LIM teardown either.

I just read the entire thread over again. I am going to have to say to check grounds, and ground busses. If that doesn't do it, I would try getting a junkyard PCM and putting it in. You may have to swap your PROM over, but the older stuff doesn't usually need reprogramming as I understand it.

For some reason I remember the voltage code being a flag that the PCM is suspect if voltage is not a problem. Also if a PCM does start to fail, it can throw gremlins everywhere, and it sounds like you are doing just that, chasing gremlins

I replaced the battery (local farm store did a warranty swap and saved me 100.00). No changes.
Checked codes again today. appears to be 15 + 16 again. The one strange thing is: It flashed the 15 three times as it should. Then with would flash 5-6 5-6 5-6. Then back to diagnostic start up. I am starting to think that yes, I have a gremlin living in the computer. My next plan is to test and possibly replace the TPS, then if it doesn't seem to be it, going for the ECM.
So I really need info on what the deal is with ECM replacement. My car has no remote or extra electronic add ons. So I cannot imagine what if anything needs to be programmed. Thanks!

Code 56 is a Quad Driver Module failure, which could be another piece to the puzzle

What I meant by 5-6 is will flash 5 times then 6 times in triplicate like any other code then go back. Does that mean 56?? TPS Metered out ok