If it is a V6 Duratec, start by changing Bank 1 Upstream O2 sensor. Then drive for a while and see if other codes return. Note that P0171 is Bank 1 lean.
Bank 1 Upper O2 sensor removal in Duratec Maintenance FAQ
http://www.contour.org/ubbthreads/showflat.php?Cat=&Board=v6maint&Number=1023736&Forum=v6maint&Words=replace%20o2&Match=And&Searchpage=0&Limit=2500&Old=allposts&Main=1023736&Search=true#Post1023736
If it is I4 Zetec, then change the upstream O2 sensor (before the catalytic converter).
Edit. You did not mention which connector you had water in, you need to check for both VSS and MLPS. The way to get the tranny codes is run a real time scan (when the engine is turned off, the tranny codes are usually erased unless it is a "hard" code).
Has the ATfluid ever being changed?
http://www.contour.org/ubbthreads/showflat.php?Cat=&Board=tranny&Number=992476&page=0&view=collapsed&sb=5&o=31&fpart=1
