From reading some other posts about this swap, seems as though the tough part of this is in the little things. Like PATS keys, clusters, GEM, and so on. The one guy who's a ford master technician did it and said he would never do it again. If you just have the engine+tranny+accessories+PCM, chances are you won't be able to make it work. The best way as I understand this is to have a complete donor car and first swap the entire subframe assembly (engine, tranny, drive shafts...) and then whatever other electronic things you need to make it all work.
If your car is running lean and has no power, I want to say you have fuel problems. Get the pressure measured. In fact if this happens to be a clogged fuel filter or a bad fuel pump, swapping in a new engine will not solve the problem. The other possiblility is maybe there's some clogging in the cat so that the engine can't breath... But that seems less likely (and your cat is covered by the 8 years/80K emissions warrany anyways).
Good luck!
Yiran