I was not aware that the GEM is a programmed device. There is nothing in the Ford service manual repair procedure about it needing special re-programming (other than the FOB TIC codes).
I know that the PCM and the cluster (PATS) is a programmed device. As such, a change out requires re-programming. This is noted in the Ford service manual.
The key FOB re-programming can be done by the owner. It does not need anything special other than a working key.
If you buy new keys from Ford, they will NOT work. For the home user, to re-program new keys requries two WORKING keys. With less than two working keys, a dealer or locksmith is needed (or disable PATS with a tuner).
From your post, I am confused about what works and what does not. I am assuming the new GEM does not blow fuses.
Live and learn.
>>>GEM programming procedures from Ford service manual.
Programming —Keyless Entry Remote Transmitter
NOTE: All keyless entry remote transmitters (15K601) must be programmed at the same time.
NOTE: All previous transmitter identification codes (TIC's) will be erased when programming mode is entered.
NOTE: To program (or reprogram) the keyless entry remote transmitters into the generic electronic module (GEM)(14B204), perform the following steps.
Turn the ignition from OFF to RUN eight times within 10 seconds, ending in RUN. If the GEM has successfully entered program mode, it will lock and unlock all the doors.
NOTE: The first TIC must be entered within 7.5 seconds of entering the program mode and additional TICs must be entered within 7.5 seconds of the first TIC. The programming mode is exited whenever the timing constraints are not met.
Press any button on a keyless entry remote transmitter, and the doors will lock and then unlock to confirm that each keyless entry remote transmitter has been programmed.
If the door locks do not respond for any keyless entry remote transmitter, wait for several seconds and press the button again.
Turn the ignition switch to the OFF position, or wait up to five minutes after step 1, to exit program mode. If a keyless entry remote transmitter has been programmed (or reprogrammed), the GEM will lock and unlock all the doors one last time.