More info:
battery = 12.53V with everything turned off
-drops to around 11V when cranking the starter
-once engine is running voltage jumps to 14.4V (alternator charging)
-don't have any way to do a load test or measure cold charging amps available on the battery (so, the battery still could have problems; it's almost 5 years old.)

Compression (no oil added to cylinders; engine a little under operating temp)(156psi listed the specification in the Haynes repair manual I have.)
#1 150
#2 155
#3 160
#4 150

I have to reset the ECU by disconnecting the battery for over 10 minutes for the engine to start cold. (I tried to start it when I got home tonight. No go until I reset the ECU.)
So, my guess is the ECU is getting bad data from a sensor and building an incorrect picture of how the engine is performing.

A tuner friend of mine suggested it might be the O2 sensor. (but, I using the same exhaust manifold and O2 sensor from the old working engine.)

After one idle session that dies when the engine gets close to operating temp, all the plugs are black with carbon (thin, flat black coating that's semi powdery).
[ATTACH=CONFIG]84018[/ATTACH]

I wiggled all the vacuum hoses while the engine was warming up (no change; so, I don't think any of those are causing a vacuum leak).

Next step maybe loosen and retorque the intake manifold (need to pickup a 12mm 6pt flex socket for this; maybe a 12mm crows foot too.)
The tricky nuts are bottom center, and the two near the PCV valve between cylinders #1 & #2.

Still without a car.
(the old D16A6 ran like a top. But, burned oil, leaked oil, and was getting tired.)