No water in fuse box or GEM but I have giant paperweight
 

Had some rain, truck acted funny. lots of clicks and buzzes but not enough juice to start. Fiddled with things (turn signals, put it in gear, hazards) and it started. No issues for a week. Another rain storm....same issues....this time took me longer, 5-6 mins...but it started and no more issues. Then a light rain, and I didnt drive it for a few days, and same issues.....this time its been 6 days and I can not start the truck.

Someone said leaky windshield. Looked and there is some water on the floor on passenger side. Drivers side is totally dry. I did some searching and it would seem to be GEM or Fusebox has water. Took them out of the truck and disassembled as much as I could. No signs of water at all. its all very dusty, but not caked on dusty like its been wet. Just dusty. I dont think water is getting in on the drivers side, although it is still possible.

Actual symptoms: when you open the door the top most relay in the fuse box clicks a lot. Occasionally it will click like a turn signal is on. There are faint lights on the dash. I am sure its a low voltage issue of some kind.

Sorry....thought I had a signature.
99 F350
XLT 7.3l 4x4 srw club cab long bed
all stock as far as I know except warn hubs and new radio.
had windshield replaced 3 years ago
no clearance lights

Don't know if you got your truck fixed r not, I had a problem with a 2000. would die on freeway at speed then start right back up. fiddled with harness behind GEM and could kill engine in driveway. pulled gem and one blade on the GEM had been folded over and the female connector on the harness bulkhead would only "kiss" the folded over male terminal. That terminal supplied power to pcm killing engine intermittently. Good luck Gem issues are a Bitch.