The business of getting wiring harness & the PCM from different cars and engines to work together sounds mysterious & problematical to me. I have fixed up two Escorts where I took the engine/transmission out, rebuilt the F4EAT transmission, put new piston rings in the engine, along with new crankshaft seals and getting a valve job done on the head -- and put it all back together completely 'stock'. Doing that suits me very well, and since we have emissions testing where I live in VA, it makes it easy to pass the 'emissions dyno test'.
I cant imagine I would -ever- put a newer engine into an Escort and leave the original Escort automatic transmission in the car. The F4EAT is a fine transmission - if you dont mind rebuilding it about each 100k-150k miles. (And I dont consider it a hard rebuild, if none of the hard parts have been damaged - like the gears in the differential).