My experience with rebuilt tranny. I had a chevy Blazer rebuilt 3 times by 2 different shops. ( yes I was a slow learner ). They always made it past the local warrany. The engine and body were good so I hated to give up on it.
I convinced myself that I agree with the above advice. Never would use a local shop again. If my f150 tranny goes out I would bite the bullet and get a Ford reman tranny with a 3 yr warranty.
I know that does not help you now. My advice would be pursue it hard and document with the shop before warranty expires. This will help if you have to sue them.