While it looked like it was not powering up, I ran a voltage check and established the voltages were normal, no sign of a short. However, because of firmware problems it was neither communicating nor blinking any LEDs. So it was actually powering up, but not showing any indication from the outside of being powered up.
There are a lot of LEDs on the Megasquirt and the Stim, but there's no LED that just indicates the unit has power. Every last one of the LEDs only blinks in response to a processor output.