For the love of God don't go through Ford. I did and I had to shell out another 2600 a year and a half later to get the job done right. They will only put a rebuilt old model in the car in place of the one already there and if it was rebuilt it had problems to begin with. I recommend finding a Transmission shop in your area that has a 3yr/36K mile warrenty on their work. Ford will only warrenty the Transmission for 1yr/12K miles. I understand fully your problems my other two did the same thing when they went out.
I wouldn't go with Ford unless they offered a longer Warrenty and installed a NEW Transmission none of this "FQR" (Ford Quality Remanufactured) or other Remanufactering Companies crap.
Problems with the other two where Torque Convertor Lockup, Transmission overheating, defective valve body.