I've been away for a while, but came back today for quick visit and saw this. Search the archives, I covered this setup once already including part numbers. But here is the gist of it:
4 bbl intake manifold
4 bbl to tbi adapter
4.3 throttle body with stock injectors
747 ECM with stock harness (or painless harness if you have the money) and sensors
Use acomputer controlled distributor from a late model 250 6 cylinder, part number available in the archives
Good luck on the appropriate knock sensor, I used the one from the 4.3, worked ok
The big cost is the 4 bbl intake manifold.
Stock chip from an 87 5 speed 4.3 liter astrovan worked best for me.

This is a whole lot harder than hooking up a holley 2300 350 cfm carb with an HEI ignition and honestly wasn't any better for performance, but it sure was cool to show people.

Megaquirt will work, the above setup is easier.

BTW, use the 4.3 setup on a 250 and LOOKOUT. Its whole different animal. Throttle response like you cannot believe.

PM me with questions if you need to.

Chris