LOL! I think we both know just enough about computers to be dangerous... which brings me (finally) to sending you some info for doing some pinout testing. We'll be working pretty much exclusively with the 60-way PCM connector unless something turns up goofy along the way.
There's a handy numbering guide cast into the connector mold on the back (wire) side of the unit... much easier to follow than the diagram connector.
Let's start with the power supplies to the controller.. there are only two. If at all possible, see what you can do to round up a headlamp or fog lamp bulb to jumper between these
feeds and ground to properly load test the circuit capacity. Your problem seems to be dependent upon having the engine running for a bit, which will load test the circuits in their own way. Pushing close to 4 amps through these wires, the brightness of the bulb will tell you in no uncertain terms whether things are in good shape or not. I'd give each circuit several minutes of test time to let things heat up and break down if they're gonna do it.
Be careful to avoid spreading the PCM connector terminals... look through your drill assortment to find something that JUST fits or is a little bit loose and use it for your terminal probe.
Pin 3 (red/ white wire) is the offshoot of that A14 splice you fixed. This circuit should be hot at all times.
Pin 9 (dark blue) is the other splice and is your key-on voltage source... the wakeup call to the controller.
Next are grounds, tested the same way with the bulb... just connect the other wire to battery positive.
Pins 11 and 12 (black/ tan) are both power grounds, just as important as the positive power sources. I'm VERY interested to see if these circuits can carry 4 amps for a few minutes. The grounding point for this might be the small 5/16" sheet metal screw on a double eyelet at the left front fender area. If you find it to be a weak ground, I'll sure investigate further.
There may be more testing later, but let's start with this. The remaining circuits I'd be interested in are Pins 4, 6 and 7 but they'd something you'll have to monitor in real time as the engine stalls.
If I hadn't mentioned it earlier, try manipulating the 60-way with the engine idling to see if it makes a difference in the way the engine runs. I've seen a number of these controllers with broken boards that are quite cooperative in stalling if you stress 'em just a little bit.
I just re-read a previous post where you said one of the powers sources were gone under the relays, but returned after cycling the key. That might mean the problem lies with the ignition switch or something along the ignition switch feed to the splice underhood. Give that ignition feed (Pin 9) a good long load test and don't be shy about wiggling the harnesses underhood and under the dash.
DD... your patience is much appreciated!