I am using Diacom scanner software.
Test one engine at a time by disconnecting the battery, then disconnecting one ECM- in a multi-engine setup, one is set as Master and the other is Slave (don't kill me for calling it this, that's the real name for it). Check in Diacom to see which is which, so you can run the Master first. It could be that the harness has a problem.
While you're doing this, inspect the ECM's pins after unplugging the harnesses- if you see any green deposits, it means that water bypassed the seal(s). If any of the pins are missing, the ECM will need to be replaced. This sometimes happens when the ECM(s) are located in a place where water can drip from above, onto the plugs.
I'll assume the Diacom has a way to see the MAP voltage and an indication of vacuum, in KPa (Kilo-Pascals, absolute). What does this show when the engine runs vs Key On/Engine Off? You should see a difference- at idle, the vacuum should be higher than at higher RPM and the voltage/vacuum have an inverse relationship- you should have high vacuum/low Voltage, low vacuum/high voltage.
Check the wiring diagram- if an engine has overheated, wires can melt and short. I was trained for Indmar injected engines, but this came from the same assembly line, so the harness and sensor locations should be the same. I would need to look in a manual but IIRC, the ECT and MAP sensors share their ground wire location.
