What I am thinking:
If you have the expertise to program an ECU, your skill level is far above that of all but maybe three of us on here (and none of those three have responded, I'm thinking Josh, Rudy or Rob).
Asking us for help when you are that deep into it is a waste of time.

On the OTHER hand:
You did not post the voltage readings of the engine control relay's output, and much of what you describe makes me question if that output is always present. Why are you looking at a relay closing, but not measuring what is getting from the relay to the ECU?

AND....
"Cooling fan will run at full speed (which might be a separate issue)." Ok, fine, maybe your knowledge is not as extensive as I first thought, just reading a few threads and you would have understood what a "warp speed fan during no crank" means.... It means the ECU is not powering up (no ECR output from the RCM) or the ECU is defective. The FCM will run the fan at high speed ANYTIME the FCM is powered up (by turning on the key) if the ECU is not sending pulses to the FCM. This is an engine protection feature of the FCM - if the FCM is not being told how fast to run the fan, it runs the fat at full speed for the safety of the engine.