From my conversation with the service writer today it seems I have to deal with Ford directly since it's their field rep. who voided my engine/drivetrain warranty. Bascially if the dealer did the repair Ford would not reemburse them for the labor/parts.

No idea what I'm going to do. I certainly don't have $2k to drop on a tranny at this time. I'll give Ford a call but even the service manager said don't expect much cooperation from them. His words were "The Ford customer service department is less then helpful".