Wow, haven't checked progress for a few days and was stunned to see what happened! Sympathies to you in the coming days with your wife

I hate hindsight because the screwups are so obvious..... and it takes a brave guy like Mark to put them up here for all to see and critique

One of the best tuners I've ever worked with was Mitch Pederson of AEM, and when he came out to give me a hand with one of my supercharged Lexus V8's on the dyno, I was amazed at how methodical his checks were before we fired the engine the first time. Before turning the fuel pumps on, he dry fired each injector to ensure it "clicked" right, and in the correct firing order. Then he pressurised up the fuel rails, turned the fuel off, and made sure none leaked.
Then we pulled all the coils and fired each coil/plug (we were running COP's) to ensure each one was sparking and in the correct firing order. He fired both injectors and coils at an artificially low RPM, using a simulator, so it was easy to visually follow the firing order.
He then checked all the input sensors to ensure they were reading correctly, calibrated the TPS and WBO2 sensors (the WBO2 was way off, BTW).
Then he made sure that both the crank & cam pickups were generating the right signals and with the right polarity (he had a toothed wheel on a mandrel that we chucked into an electric drill)
In retrospect, he was simply following the correct commissioning procedure that one would do for any expensive piece of equipment (like a gas turbine, etc.), prior to running it for the first time.