Older points ignition vehicles used a primary ballast resistor to keep the coil from popping with the key ON, engine not running.

Electronic ignitions have the choice of not driving the coil except when the engine is running, using a ballast wire/resistor like the old days, OR using active current limiting when there is no RPM signal.

Anyone know what Ford's PCM does?

You said the ECU was changed, but was the PCM changed?
If you leave the key on, but the engine isn't running - after say 5 mins are your coilpacks HOT?

 

Did you figure out this issue? I have a similar issue.

 

Guess I'll add my 97 ranger to this problem. Been through 3 oem coil packs. The original, truck was running good, then dropped power and running rough. Couple miles later stalled, wouldn't start. At first I thought fuel pump because there was no fuel pressure. come to find out, the #19 25amp fuse in box on the side of the dash was blown. I had 2 other used good oem coils and truck has killed those and blown the fuse. Every time the coil cracks around the middle coil. Ohm test confirms middle coil is dead. And 2 of them have ozzed some white substance out the bottom crack. I put in a blue streak and truck ran fine for 50 or so then same symptom, lost power then quit, blew the fuse. This one didn't crack like the oem ones. I did the ohm test on primary and secondary and checked out okay. I ohmed the wires from the plug in to the pcm and those all were .06-.11. I have a 95 4.0 and checked those wires and similar readings. I do have another pcm in a 97 b4000 that also is a 4l and 5sp. guess I will try that.

 

A possibility might be poorly seated plug wires. Spark jumping the gap in the coil pack towers can cause heat that causes failure. Just a guess. I'd make sure I had good wires firmly seated next time. The fuse probably blows after the coil pack fails internally and shorts to ground. Good luck.

 

I got it figured out. The grounding wire for the middle coil pack, yellow/white stripe, that goes to the pcm, is grounded out somewhere in the harness. This was causing the middle coil to continuously fire off, causing the excessive heat build up and eventual cracking and killing that coil, drawing extra amp and blowing the 25 amp fuse. The wire must have started out occasionally grounding and at the end was always grounded. The first few coils, the truck would run fine then after a short amount of miles would run rough destroy the coil and blow the fuse. The last few coils the truck would run rough right from the start and after a couple minutes of running destroy the coil and blow the fuse. I cut the at each end and spliced in a bypass and truck has been running good.
To find out that the wire was grounded, I took my test light and connected to the positive post of the battery. I disconnected the harness from the coil and pcm. Stuck the probe of the test light into the corresponding hole on the pcm plug. The wire for the middle coil lit up the test light which it shouldn't have because the coil plug end was open. I originally had a metal tab in each of the coil plug end holes and ran a wire to the negative post of the battery. This was done to make an independent circuit for each wire to test it under a small load, the test light. The yellow/white wire for the middle coil would light up the test light when I tested the yellow/red and yellow black wires, which it shouldn't have.
I would have liked to see where the wire is grounding out but I'm not pulling that whole harness out and dissecting it.

 

Good troubleshooting & feedback.
If the itch to know just won't go away, you could rig up your test light & or a 12 volt buzzer in series with the lead, to also sound the grounding as you squeeze or flex the wiring harness run to narrow down the problem area.
Bends, or areas that touch something that flex, vibrate & or is hot are known trouble spots.

 

That should have killed the spark on two cylinders since spark happens when the circuit is opened. Make and break. If there was a permanent ground there's no breaking of the circuit. Maybe when you changed the coil pack you removed the short to ground, then when it reshorted the center coil overheated. Suggests that the short is close to the coil pack.