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I have a 2000 f150 5.4 xlt. Auto. Last week a big rain storm, and yes my windshield does leek a bit (getting repaired ASAP) and all of a sudden my head lights flashed on/off until the battery died. While this was happening you could hear a relay somewhere going off, and it didnt matter if the h/l's where on auto/on/off, they kept flashing. Rain stopped, i jumped the truck and it ran fine, expt the Auto lamp feature does NOT work now. Not sure if i have a bad relay, or sensor but all fuses seem OK. I assume water got in somewhere, as it would be too big of a coincidence. Also to add, out of nowhere my power windows and interior lights(dome, hood, door) stopped working. everything else is fine. I think it is another relay, but not sure. Just looking for a direction here. I am not sure how to test a relay. thanks.
There is a black box under the dash called the GEM module. It controls all the electronic convienence features of the truck. And it's usually right in the path of a windshield leak. It mounted to the firewall under the dash. See if you can find it and see if it has water damage. Also check the fuse box, It can have water damage too.