Check TSBs
WARNING: This page is about a different car, the 2005 Ford RV Cutaway, 2005 Ford Econoline, 2005 Ford E450 Super Duty, and 2005 Ford Cutaway. However, it is still accessible from the selected car via links, so may be relevant.
Refer to all Technical Service Bulletins (TSBs) that pertain to the transmission concerns, and follow the procedure outlined.