I wouldn't know where to start as I've been through this car thoroughly front to back. The car has 53k original miles with no rust whatsoever. Everything works that's electronic. The car ran perfectly before adding boost. There were no ignition problems.Voltage drop tests, test the entire power circuit. It's not specific to the coil. I would recommend watching some YouTube videos to get an understanding of it. If you have a ground issue, the spark has a hard time completing the circuit which could be where your problem is coming from. There are so many people who run stock ignition without a CDI which is why I'm suspecting something else.
I would think that poor grounds would affect the Megasquirt as well. I have all of my gauges grounded to clean sheet metal at the tranny hump. That shows a good ground plane.
I'll test voltage at the coil plug tomorrow.