4.8 in boat poor idle, won't rev

[squared]

Initial installation, trying to get it running correctly. Engine starts with high idle, eventually drops after going into closed loop. The idle is steady until you tweak the throttle, then it goes into a constant periodic surging. When I open the throttle, the engine will not rev, it starts to build, but then chokes out and enters a more dramatic surging than at idle. Occasionally backfires through intake.

Injectors, throttle plate all cleaned. As you can see, the STFT is out to lunch significantly. The O2 numbers as well. I've checked for vacuum leaks, fuel pressure (45-50), etc....all good.

I am getting an intermittent pending CKP voltage code which clears, but has popped up inconsistently. Have utilized the scanner to disable each injector, and am getting an rpm drop on each cylinder. Have also played around with spark advance in the controls section, when I disable absolute advance (can't remember the exact wording in VCM), spark advance drops to 0 and I get an associated rpm drop.

I'm assuming I need to do a new case learn, but I can't get there if it doesn't respond to throttle inputs.

Attached scan files. On the second run, bank 1 O2 sensor lead rubbed on the alternator drive pulley and cut through the wire insulation, so that sensor data is erroneous.

Configuration:

I've replaced the 5.7 in my wellcraft with an LR4 that I picked up at a salvage yard last year. I bought the complete engine with coils, injectors, sensors, etc. Also bought an 0411 PCM, but was most likely not from the same truck. The harness had been chopped, I rebuilt the harness by soldering/shrink wrapping new wires to the existing harness with pins. Engine has been rebuilt with new pistons, bearings, valve job, etc.

In order to minimize installation variance issues, I've retained as much of the original "configuration" as possible except for EGR and EVAP which are not connected. I'm using shorty headers inverted with O2 sensors in the riser. I am running a MAF. Coils are mounted on a bracket I've fabricated, attached to exhaust manifold studs. EGR intake port is plugged.