It won't help if I sent it direct to you, but I have a spare ECM as well, with the stock tune on it that I would be happy to send to GDE for you. The reason it would need to go to them is that they can re-code the stupid security coding with your vin#, so that the ECM will actually allow the engine to run longer than 3 seconds.
I'd be shocked if it was the ECM, but at this point... I'm willing to grasp at the same straws you are. I'm NOT thinking anything mechanical anymore, the engine sounds just fine without any fuel going into it.
The fact that this all happened at speed and with the engine running normally prior... Says that if there had been a loss of compression, you would have found the reason already - Probably via a newly-installed inspection hole in the side of the block.

Since that hasn't been found, I'm gonna pull my money from the "messed up internals" column. The odds are too long on that now.
I realize it has been a VERY long time since we talked about fuel as a problem, but did you ever set up a dedicated "IV bottle" direct into the CP3 and give that a try? With fresh and shiny injectors, it will take a lot of cranking to clear the air from the fuel rail, BUT I think this might still be a worthy endeavor IF you hadn't tried that before. The RPM changing when you unplugged each cylinder is interesting - Rising RPM would (to my thinking) indicate that the cylinder is now not fighting to compress anything other than air (liquid doesn't compress, but if it was fuel it should go boom) and so the engine is able to turn easier without that resistance. Each cylinder should have been injecting fuel, and unplugging the injector should make the RPM dip, not rise.
That just still makes me wonder what is in that rail. Yet the other side of the argument is that the rail feeds all 4 equally - So how would #1 be able to run at all? When you unplugged #1, the engine ran like CRAP. Obviously #1 was doing the lion's share of the work, but the engine STILL maintained operation, right? If the two (assuming for a moment that only one cylinder is actually failed) remaining cylinders are only 90 degrees apart in sequence, then the idle would be VERY uneven.
Never mind - I don't know where I was going with that reasoning anymore, I can't figure out a logical way to eliminate any of 2, 3, 4 from the problem list. LMK if you want the ECM, or if you want to wait for the compression test. I also have a mostly-complete wiring harness, I removed the two airbox connectors for my own CRD. Everything else is still there, if you figure out that you need that. The two connectors are easy to replace.