No spark or 5v ref; Works correctly w/ stock ECU
 

I have a 1999 Miata with an MS3Pro PnP. The car has been running fine on the MS in the past. Last month, my poorly-built engine seized on the highway, and I sent the car to a shop to have a new engine built and installed.

The new engine is now in the car, but will not start because it's not producing spark. No 5v reference to the sensors. Because of this, I'm getting nothing on the composite logger. No cam, no crank. nothing.

When Megasquirt is pulled out and a stock computer is plugged in, we have 5v ref and spark. Will not run on stock computer because of modifications (injectors, trigger wheel, WBO2, etc), but there is 5v ref and spark.

Considering that the MS worked fine in the past, was preassembled PNP, and the 5v ref is correct with stock ECU, I'm at a loss for what could be wrong here. Nothing has changed ECU/wiring wise between last month and now.

Any troubleshooting suggestions would be helpful.

Thanks.