Some years back I bought a 1990 Ford Aerostar from a used car dealer but it had some factory warranty remaining. I had transmission problems and the Ford dealer rebuilt the transmission under warranty. The first time the dealer rebuilt the transmission it wouldn't go into overdrive. The service manager found the overdrive band on the technician's workbench so it had to come apart again. However from that point on, the transmission worked well until I sold the Aerostar 100,000 miles later.
On the other hand, I had engine problems under warranty. A cylinder head had a crack and in stripping down the engine, the service manager reported that a cylinder wall was scored and the entire engine would be replaced (this was also under warranty). I asked the service manager why they just didn't hone the cylinder wall and he said that Ford wouldn't allow this. Of course, I was delighted to have a new engine.
My experience with Ford on major warranty problems is that they seemed to do what was right. A good technician will probably rebuild your transmission correctly.