Easier then you think... with your same exact setup (starter relay signal feeding your 5 pin relay coil, then using 87a as an output) you can provide the HEI override pin 5v from the megasqauirt when not cranking just as the diagram intended.

The opposite of an opposite is the original, so to speak. If it were me I'd switch to this scheme - while your way works it could have unintended consequences later.

Once you have the efi / megasquirt thing down you won't have to worry about firing a new build on computer controlled timing. I've been using EDIS + Megasquirt for a few years. On my new recent build it fired first crank.

Get in the habit of saving your tune after every change for reference.

Random thought - you just put efi on a car that never had it, and your spooked by someone else's previous dash wiring hacking?