Just for you keyless entry ...
I was having the same problem for almost a year until I found a secure way to work it out.
My doors, trunk and alarm were dead with my remote. After some research I had found many information. Behind the glove box, the small box on top the ECU is the security/alarm module, don't bother it. Ford may charge you some big bucks just for the diagnostics.
There is a fuse (#63 central locking system on the manual) ... behind the fuse panel. To check this fuse you have to remove the panel right below the steering column, there are four bolts to remove that piece. Then you will see the whole fuse panel, in the middle and at each side you will see a small bolt to remove they are (2) very easy to turn after you loose the first turn. Then look for the white tabs in the four directions, these plastic tabs are part of the panel that keeps the piece attached to the metal support, prick all carefully and the fuse panel just fall down for you with a big mess of cables and conectors. Turn the panel so can see the fuse, it is in the oposite edge to the small black box ( timer/bell ) it's is yellow 20 amp fuse hard to extract from the recess, just check and change as needed, it's similar to the ones fuses in the front but different rate. If the fuse fry try the self test for the doors and switches to find the problem, do not force the fuse because it will fry your pc for the alarm.
Then all you have to do is to re-asemble back all the pieces, be gentle with the cables and connectors and with your bolts and screwdrivers, before you tighten check the path so you dont kill the edges, all this bolts are metal on metal and very easy to kill them with just one bad turn on the screwdriver.
Hope this can serve you well or sent a pm for a picture.