just because the dealer is where you took it doesnt mean the dealers trans builder has a clue how to put together one of these automatics correctly (obviously)
from what I have been told and seen the Ford V6 A4LD family is a real tricky little unit to get correct, the tolerences internally are much more stringent then that of your run of the mill full size auto or chevy automatic, so it takes someone who has been kept up to date on all the updates and internal upgrades, no corners can be cut, and attention to detail must be paid, or you end up with the nightmare you are experiencing with your automatic. I would seriously fight the warranty dates on your unit, just because they give you a warranty that starts on teh day you pick up your rebuilt unit, does not mean it should not be extended if they cannot get it right in 2 attempts