I read through the documentation of the MS3Pro last night to try and get an idea for how it works. It looks like you can adapt a points distributor to function as a camshaft sensor using a Hall effect sensor. OP's setup for the crank is the only setup I can think of to get an accurate reading of crank timing on a /6.
I see little benefit to the Ford EDIS system from what I was reading, since LS parts, especially coil packs, are readily available and the MS3Pro can easily control them for sequential ignition.
As far as setups go, this makes sense to me. I've been looking at switching to EFI for a while, and the Sniper/FiTech systems just don't seem worth it, they're glorified carbs, whereas a proper ECU controlling injection and ignition can adjust spark and injection timing to get better, more efficient performance across the entire RPM range.
I'm definitely interested to see how the OP does coil-on-plug mounting for this.