I'm glad you were able to resolve your issues by identifying the water damage on your GEM Module. Yes, a backup GEM is always a good idea. Now it looks like you need to find and fix that leak.

The bottom picture I see no problems except those customer access wires should have some shrink tubing on their ends to protect those circuits.

The top picture I can't quite make out what that wire is to. Someone may have cut the 'key in ignition circuit' wire to get rid of the dinging sound when the truck is off and the key is left in the ignition.

Drake

 

Are those wires the pass through wires for making a connection from the engine bay to under the dash? Look in the engine bay side where the pcm connects and see if those are the same wires that are hanging there.

 

Do you know if the new gem will have to be reflashed?

the wires that need to be taped off, are those for a trailer brake controller? I will be installing one this next couple months so if these are it that's great.

And good point on the single wire picture. The truck does not chime when the engine is off and key is in the ignition, I'll have to check for this.

Robbragiel : I will try and trace the wires. The problem is that there is only a few inches visible and after that they go into what looks like the main harness and its all wrapped.

 

See if the wires are the same color on the engine bay side.

 

Thank you so much for this thread!!!! I am going to try and clean my GEM as well!
Do you happen to know if the GEM would cause any fuse boxes to not read in some fuse ports but will read in the other ports? For example, I have 3 fuses in the CJB in the engine that are in good condition but do not read with a circuit tester while the fuse is in the port. I took out the fuse and tested the port itself and that would not read either. When I tested the fuses that would read, the ports would also read as well.
Now I have many fuses and the ports not reading in the passenger compartment fuse panel but it reads the same as explained about the CJB. Super confused on this....
In addition, do you know if there is any way that the fuse panels can be cleaned and still work as well?
I have also researched and found that Ford issued a message (#15733) that states this is common in my model truck (2000 Lincoln Navigator 5.4) because of a leak in the windshield. I saw other posts that said theirs leaked from various places. My plan is to use silicone on any openings, seals, and my roof rack to hopefully help keep water from getting in. :/