I'm sorry to hear that. I wish I had an answer but I am in a similar situation, but every time I had my transmission checked due to a sound right before changing gears all they did was reset the computer telling me that everything was working fine. Right now I am just waiting for a service rep get back to me and see if they can replace the TCM since it is under the recall but my car is from 2011 and only has 79K miles on it. The car drives fine and changes gears fine, just that annoying sound that goes away if I press on the gas a little more and changes gears.
If they wont cover the replacement parts and say that is still working and is safe to drive (I will request a written statement before leaving the dealer), I will drive the car until it dies, and if something happens due to a bad transmission or TCM I will make sure Ford pays for a new car and what ever expenses. They always told me it was fine and there were no problems with the transmission and not to worry about it.
If they wont cover the replacement parts and say that is still working and is safe to drive (I will request a written statement before leaving the dealer), I will drive the car until it dies, and if something happens due to a bad transmission or TCM I will make sure Ford pays for a new car and what ever expenses. They always told me it was fine and there were no problems with the transmission and not to worry about it.