I just spoke to my son about my 2003 Expedition keyless entry system as my battery had gone dead asand quit working. I replaced the battery and he said to do the following: get into the car, turn the key on/off 8 time within 10 seconds ending in the on position. The door locks will activate, within 20 seconds press any key on the FOB and the door locks will lock/unlock to acknowledge that you FOB is set.
don't know if it will work for you but worth a try. | 
