Interesting problem to say the least. Two years ago I replaced the heater core by pulling the dash and putting it back. Ever since I have had weird accessory issues, such as: The AC panel lights do not work, the windows work regardless of if the car is off and door has been opened. When the car is turned off the radio turns off when before the accessories were delayed from powering off. The alarm system operates weird. Hard to explain but, I can only disengage the alarm by using the remote, using my key in the door doesn't disengage anymore. Most annoyingly the door chimes whenever I have the driver side door open. I am open to any suggestions, I really want to avoid pulling the dash off to try and fix this... I will say when I finished up there were a handful of leftover screws. I have searched the internet for hours on this one. Things I have checked: Both the ground wires that are under the driver and passenger side kick panels visually look good. I have gone over connectors and think I got them all. I visually inspected fuses in the cab. I am open to any suggestions!

The truck in question is a 1998 Ford F-150, 4.6

 

Have you checked the damage to the GEM? Specifically if it's damaged or has water ingress?