I'm going through the same problem, I think -- bad shifts when throttling. I am out of warranty so I haven't been dealing with a Ford dealership but a local service garage. Anyway, after a lot of transmission rebuild the problem came back, and it appears that it's related to cracking of the wiring in the main sensor wiring harness and injector wiring harness. Manual tape-up of this wiring doesn't work very long, as you might guess.
I found this recall:
http://www.contour.org/FAQ/recall/99M03/
I also have these part numbers:
Main Sensor Wiring Harness
F5RZ1EA581S6A
Injector Wiring Harness
F5RZ9D93S6A
However, I can't even find these used on the entire interweb so far.
If I can't find these my only recourse is to buy new parts, which are in stock but will apparently cost $2000.
Ugh!