Ford ecu all the way
Ford Pats immobilizer can not be diy bypassed but can be used.
http://youtu.be/Pxq4ks2Us_U
http://youtu.be/BKqeCjdBM0w
Manifolds arnt important as long as the ecu see's the info it wants from its sensors. As said in closed loop it will pass Iva and run well. Ive done one and seen it through Iva and mine should follow soon. The ecu will run with jenveys, bike Tb's or a log manifold if the ecu has the info it needs.
It will also be down on power compared to your omex but not by a huge amount. On the plus side rolling road time costs money and the eec-v doesnt need any
This is just my opinion, I am biased and dont like Megasquirt.