I have a 2007 Whipple 496 with PCM 555. Going through the five zone the other day, my engine made a "pop" and stopped running. Before and into the 5 zone, oil pressure, fuel pressure, engine temp where all good. It restarted for a few seconds and it shut off. It would crank, but not start. When I turned the key to the on position, I did not hear the fuel pump priming. I swapped the two relays next to the PCM. Still no fuel pump. I pulled the fuel pump relay and jumped the fuel pump and let it run. The engine would stumble and not start. Fuel in separator was full and clean. I have a Rinda scanner. When I put initially put it on, it read the PCM and I had no codes. After testing for the problem, the scanner now says "cannot connect to any ECMs". The fuel pump does not prime and now the gauges are not getting a signal. I just put in a new fuel and power relay next to the ECM. No luck. The fuel or main relay seems to have a faint buzzing sound, just like the old relay when this problem first started. I have power at the key, at purple wire and it will crank, but no fuel prime, no PCM and no start. The kill switch, neutral switch, fuel pump fuse and 50 amp breaker are working correctly. This engine only has one fuel pump because of the Whipple. Does the purple wire from the ignition go to the 10 pin harness? I read pin 5 on the DIN should have power with the key on. I unplugged the DIN and it doesn't. I only have the 12v power on the DIN plug with the key off on connection 6. How does the PCM get powered up? I read the PCM creates a ground and it may have burnt and is not working?

Does the tach move when cranking?

I don't think so. I also tried it disconnected. I'll recheck.

Looks like your Starting/Charging harness has power because you get the crank. Maybe just the ECM harness is without power? I would start checking the grounds on the ECM harness and the power connection between starting/charging harness and ECM Harness.
I'm not a tech, just my 02.

Edit: Or if you have no power at the purple wire with the key on, maybe your problem is there. The starter has power directly from the battery, so if your key does the start position, it will crank. Maybe you just have a faulty ignition key switch?

@AP700. I do have power on the purple wire at the ignition with the key on. No fuel pump prime. Engine will crank strongly, but not start. I believe the PCM creates ground when it is powered up. In Mercury manual #33 it looks like pin 1 on PCM harness #A should have power from purple wire. I'll check that this morning.

Hopefully your IAC did not take out your PCM

If you can't figure it out I would highly recommend John Mosetti at Boats Unlimited in Texas. He's the guru on the 496, especially electrical, and rebuilds the PCM555s constantly.

I thought he sent them out to some place in New York???

If you have no tach signal then ECU doesnt command fuel pump, spark etc ...IE no start .
If your tach doesnt move while starting you have no tach signal.
If you have a distributor with a module , module is most likely dead.

No he does his own repairs.