TECH TIP #1: Always reset the Fortin module before any reattempt at programming the system to the vehicle: Disconnect all plugs from just the EVO-ALL module: Press & hold the programming button on the module and insert just the harness's small black 4-pin plug: Release the button when the specific color of LEDs lights up as indicated in your installation guide: Proceed to key programming steps as indicated in your manual.
TECH TIP #2: Timing is crucial for proper key programming on the EVO-FORT4 system: When each key is turned to the on position, count 3 door chimes as an indicator for proper timing.You will know that steps are being performed in time when you get back to inserting key #1 for the second time; by hearing or seeing the power door locks in the vehicle cycle from lock to unlock on their own. This is confirmation that you have entered Ford's 3rd key programming mode within the proper time. Even with the module disconnected, using the 2 keys, you should be able to cycle the door locks with the keys and get the vehicle to enter programming mode. This is a concern within the vehicle and not dependent on the module itself.
If the vehicle's power door locks do not cycle, the problem could be:
A) You do not have separately coded keys; you have a cloned key with the same anti-theft code as the first key. To enter the vehicle into programming mode, you must have 2 keys with their own individual anti-theft codes programmed to the vehicles to put a Ford vehicle's BCM into programming mode.
B) A common issue on Fords is sometimes the ignition will stay on or cause a delay during programming; if this is the case, reset the module and try going through the programming procedure again, BUT this time leave the RED connector unplugged from the module until the module programs, then plug the red connector back in.
C) Another common issue with FORD vehicles is that their Key Sense wire drops out intermittently. This is a problem with the vehicle itself and not the module. Reset the module (see tech tip #1 above) and try going through the programming procedure again, BUT this time keep inward pressure on the key so that the key sense signal never drops out while the key is in the barrel (you need to hear the vehicle's key chime each time to confirm that the key sense wire is working properly). Do this while redoing the programming from start to finish. Manufacturers TSB link 
D) The vehicle's battery is too low. A standing voltage reading below 11 volts will prevent the system from programming and/or working properly even after successful installation. Additionally, the vehicle's BCM may not communicate properly while the vehicle's battery is being charged.
E) In rare instances, the Ford vehicle's BCM has been locked by the dealer against entering programming mode to program new keys.This can only be changed by a Ford dealer or automotive locksmith using a dealer scan tool. Even with the module disconnected, you should be able to cycle the keys and power door locks as indicated above to get the vehicle to enter programming mode. This is an issue directly related to the vehicle and not dependent on the system itself.