If they replaced your tranny at the ford dealership they should have seen that there is a TSB Technical Service Bulletin to reprogram the PCM(computer) after replacing the transalxe. And another TSB for eractic/late/or harsh shifting to reprogram the PCM as well. Cant remember if the reprograming number is the same. But there should be a simple solution for you. I work at a Ford Dealer in Omaha NE

1998 Contour V6 se ATX Black Bassanni w/o resinators, modified intake box, DMD New headlights w/ silverstar 9005's, blue neons inside, metal waterpump, pioneer head, pioneer 5x7 3 ways,2 10" subs, 800w amp, 17x7.5 motegi mr12 p215/45/17