What do I do if I am told by Ford that they can't fix my upshifting issue?

I hope you have records (receipts, etc.) of all the visits, discussions, repairs and part replacements. This will show that you reported the problem while the vehicle was in warranty and that Ford failed to perform on the warranty. Contact someone in corporate management (this info should be in your owner's manual), and tell them that your next contact will be with an attorney. (I have a friend who had an unresponsive insurance company, relating to a storm damage claim {tornado}. He put a large sign on his front lawn, took a photo and put it on Facebook. Claim was settled shortly thereafter.) You do not have to take "I don't know what's wrong" for an answer.