After 1 month and 1 day, I finally got my car back today. They worked hard to fix the problem, but Ford was the reason that it took so long. The service tech was only allowed to perform the work authorized by Ford, and they spoon fed the authorizations one part and piece at a time.
I believe they knew exactly what needed to be performed to fix the problem, but were hoping that any one part might do it and save them money.
The clutch pack that was removed, was "blue in color", it had gotten very hot, leaking seals, shift motors stuck, and finally after rebuilding the transmission 3 times, they authorized replacing the transmission.
It drives like new, but then it does have new clutch, transmission and shift motors.
It is good to have it back.