I assume you're watching A/F ratios? What are they at?
I've seen voltage regs do a lot of funny stuff; when they aren't working right they can overvoltage stuff and fry it, damage it, etc. They can also go low and cause electronics to not work reliably; particularly the relatively sensitive Megasquirt.
Try starting it and unplugging the battery and see what voltage runs at, if it stays running (as much as it did), etc.
What do your plugs look like? Try cranking with each plug in the cable and layed out on your valve cover to confirm all 6 are getting consistent spark.