MS3 , Multiport & turbo build

While waiting for OP to answer about the ignition, you might peruse www.megasquirt.com to learn of crank-triggered ignition options. Most use a 36-1 (or 72-2) toothed wheel on the crankshaft, with a pickup, either 2-wire VR or 3-wire Hall-effect (most Chryslers). The megasquirt processor can accept that square-wave signal directly, using the missing tooth to locate TDC. If you want a dedicated processor, a Ford EDIS 6-cyl box might be used. Its output can drive a coil-pack for "wasted-spark" firing (2 cyl at once). The Ford coil-pack looks a bit goofy IMHO, so I might choose use a Chrysler 3.3/3.8L coilpack. If you want to spark only on the combustion stroke (little advantage), you also need a camshaft sensor. You might adapt one to fit in the distributor hole of a slant, or perhaps modify a slant distributor to work thus. Another little processor would have to "vote" on the EDIS output based on camshaft position, or run it all thru a megasquirt processor. For single-spark, many like the Chevy LS coils which pack a punch and have an integral coil driver so just need a logic-level input signal.

So far, I installed a 36-1 wheel on my 1965 Dart 273, but haven't used it yet. I've pondered that for my 1964 Slant but a bit harder since little room at the front and fewer mounting points for a sensor. In the small-block, I can also leverage the distributor for a Magnum which has a camshaft sensor (for sequential FI, not used for spark).
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.