I am rebuilding my 393w stroker to be a 427w. I previously had an Edelbrock Proflo Efi, but it is now dated (narrow band O2, etc). I have been researching high performance after market on hot rod forums (SB Ford, ford muscle, etc) and the concensus is that multi port efi is more efficient and can produce more power than throttle body based injectors.
I am going to scavenge my mpfi manifold and throttle body from my previous set up, and go with a Holley HP computer and harness. I'm running 10.5:1 compression and want a precision system with spark and fuel... going as far as a crank trigger wheel. I plan on over 520hp. I looked at FAST, MegaSquirt, Edelbrock, Motec, AEM; the Holley was very comprehensive (even has knock sensor capability) and very reasonably priced.
With so many people happy with Ford efi I don't think you can go wrong. If you are building a performance engine aftermarket has better options. The set up and installation of the aftermarket stuff seems simpler to me.
Good luck,