Problem with key fob
 

I recently had to replace the smart junction box my 2006 Fusion. Since replacing it, I can't lock or unlock the doors, open the trunk or set the alarm with the key fob. Does anyone know why this would happen and / or how to fix it?

Have you tried another battery in the key FOB ?

Yes. I should've mentioned that I have 2 fobs and neither works since replacing the junction box. I replaced the battery in both and no luck. My son seems to think the fobs may need to be reprogrammed. If that's the case, I was hoping someone here would know how that's done. I can always take it to a dealer but was hoping to get out of it cheap!

Step-by-Step Programming Instructions
!. Close the car doors, then open the driver's side door
Press the UNLOCK button on the driver's side door.

2. Next turn the ignition from OFF to RUN 8 times.
do this within 10 seconds, making sure the 8th time ends
on RUN. When you entered programming mode,
the door locks will lock and unlock. (Note: if the doors
don't cycle, turn the key faster. Your car may not have
keyless entry if you still can't get the door lock to cycle.)

3. Press any button on the Ford remote to be programmed.
Do this within 8 seconds. The door locks will cycle again to confirm
.the keyless entry remote is programmed and ready to use

4. Have a second remote key Fob, Again, press any button
on the remote within 8 seconds to cycle the door locks..
Repeat this step for any additional key Fobs.

5. Finally,turn the ignition to OFF. The locks will again recycle
to confirm programming is complete.