Alright, still chasing this fault. Confirmed the coil is not the issue. Original coil measures good in all voltage/resistance tests (from manual) in running and symptomatic conditions. Due to an ebay error I now have 3 motorcraft coils

. Went ahead and installed a fresh NOS one anyways. Cleaned all grounds, no issues there. Ground resistance from battery to distributor housing is near zero.
Confirmed there is no pulse 12V signal to the injectors while symptom is present. The fuel pump does not buzz when ignition is turned on. Confirmed both EEC and fuel pump relays are behaving correctly.
Tested voltages at the ECU connector (unplugged), and confirmed it gets 12V constant, switched, and good ground. The PIP pulse signal however was flipping between 4V and 5V, instead of 0V and 12V. Might be that my digital multimeter can't read fast enough and is averaging, or might be weak PIP signal of some sort?
Confirmed the resistance of the PIP wire from TFI module to the ECU is near zero. So it's not a wiring issue.
So at this point I think I need to read the PIP signal voltage while the truck is running and while the symptom is present to see if there's a difference.
I
just replaced the TFI and trigger coil with NOS Motorcraft parts, so it doesn't seem very likely that I'd be unlucky enough to suffer an original part failure AND a replacement DOA back to back.
The symptom is also no longer heat related. It'll happen when the engine is dead cold, sometimes. It runs happily until I shut it off, hot or cold, and then it won't restart. So it doesn't make sense to me that any of these components are being affected by heat. There's something about the transition from running to powered down to starting that is causing this.
I suppose it could be the ECU, but want to make sure it's getting a good PIP signal before I go there.