The ECU can be installed safely inside wherever you want. The waterproofness comes from the Ford EDIS coil packs which can be fully submerged and not miss a beat, as long as the rest of the engine is well sealed. There is no air meter to deal with either. Massive boost in ignition voltage so you can run a wider plug gap as well. Full tunability, which means you can run dual fuel maps, one for power and one for economy.
I have a 14cux plenum on my 4.6 at the moment but plan on running the GEMS 4.6 plenum and intake with the MS setup.
On mine I have the edelbrock performer intake and a holley carb, so for me it would mean sourcing a whole top end set up. It's one of the reasons I had been kicking around a bolt on set up using a GM TBI set up.
This is not the direction I was expecting when I saw the thread title.. especially after seeing that Dan posted in here.