hello! i have the phantom wiper/int lights/4x4/power windows problem due to the leaky windshield. anyways i replaced the GEM module with one from a junkyard and it didnt fix anything. someone mentioned to me that it might need to be reflashed to work with my truck by the dealer (trying to avoid working with them since im not in the habit of throwing ridiculous amounts of money out the window). has anyone done this repair and had to do that? im thinking that A. yes, it needs to be reflashed or B.the junkyard GEM was bad also or C. i screwed something up installing it.

the numbers match on my GEM and the junkyard one so i dont see why it wouldnt work but who knows...

 

I do not think that reflashing is necessary; since the GEM box is merely an interconnection interface. However what you could need is either replacement of the relays in the box under the dash (power fuse/relay cabin). When the GEM acts up is puts out power surges into several circuits that cause sparking and chatter of the relays for the window, power lock, (ext.) lighting circuits of which most terminate in that power panel or cabin.
Do you know how to service a relay? I can save you a lot of time and expense. If you check in the cabin there should be several "Bosch" type SP,DT 30A type relays; maybe 4 (based on your truck's options) at the far left. At least two control the power window function, and several other control the ext Lighting circuit. What I suggest for general preventative maintenance is to clean all of the relays in that box. The relays themselves can be disassembled removing the top covers that expose the internal switch contacts. A very small flat blade screwdriver placed around the "bottom" of the relay will be able to shoe horn the covers off of the Bosch type relays. To properly clean these you will need a small piece of fine sandpaper with the smallest grit that you can find. They do make a contact burnisher for this task, but if you cannot find one use the sandpaper. You will be able to see that contacts since they will now be exposed; so what you will do is pass a small piece of the sandpaper between each contact point. Strip a tab of sandpaper material into a 1/4" strip to fit into the contact point area. Work the sandpaper strip between each contact point for each relay, and either spray the contact with your choice of WD-40 oil or an Electrical Contact Cleaner spray, and then replace the relay's cover.
Do this for each relay in your cabin so that all contacts are fully cleaned, and lubricated then replace the relays.
This will also or usually remedy the "Air Bag" Diagnostic alarm that sometimes activates when there is a problem caused by the GEM. When you replaced the GEM unit it probably wasn't necessarily defective, but the contact plug jack connector had become wet and conductive which caused the problem initially. If you had not replaced the GEM unit before now spray that GEM connector(s) with that WD-40 or Electrical Contact Cleaner Spray. Do not use Carb. Cleaner since it will usually damage the plastic of the connector. Finally replace or fix that windshield mounting putty at the firewall or this will be happening again.