MegaJolt (and MegaSquirt) need a trigger wheel on the crank. You might want to be using electronic (Hall effect?) points rather than mechanical and use this as a signal generator. Unless you fit a vacuum sensor (and no reason you couldn't), you'll be limited to 2D advance correction, which is a straight replacement for your mechanical system.
I think it sounds like a great project as long as you know what the transistor module thingy is sending to the coil pack. MJLJ uses Ford EDIS to control the coil pack which is an extra expense you could be saving if you build this using Arduino. I say go for it and report back... (but wait for me to sell my MJLJ first!)