They did say they could flash it for whatever would best suit the setup so no new ecu. I'm kind of still debating if just a new cam and maybe porting the heads would be more worth while. I mean I've put so much money into this 2v setup I wonder if it'll all be worth it in the end.
About dropping a 5.4l in a mustang, depending on what year, if it's 9X-04 with a 2v, it will require a few modifications especially manifolds, a hood and a custom air intake unless of course you get something like this (kick @$$ looking) one:
my dad tried it with an 03, but sadly we never had time to do it, or really the equipment. I wouldn't know about dropping in a different engine (3v/4v) into the same body style or any engine into the later models but I'd have to assume it'd be easier but don't quote me.