I had the same issue, and my car is/was bone stock. There's a circuit board behind the carpet on the passenger side of the trunk with 3 electrical connections. In my case, the board was still good, but somehow lost it's callibration. Ford recallibrated it for $125.00, but if you need a new board, it's a $400+ part.
I had no brake lights, no rear turn signals, the tail lights wouldn't shut off, I couldn't pop the trunk with the key fob or inside the glove compartment, so you'll need to use your key. I also couldn't put the car in gear as the gear selector button was stuck. What I did find, was that I could turn the key to the ON position and then put the car in gear, and then start the car. This way I could at least drive the car to the dealership as nobody else can recalibrate that circuit board. All of my fuses were find as well.
Hopefully this post helps you.
Mark