I have an 03 f150 5.4 triton. Been running fine. Then it rains one night. Next day i take off and i notice its idling a little rough. Then i notice its kind if sputtering when i accelerate. Service engine soon light comes on and starts blinking around 60mph or so. I checked air filter fluid levels etc. Everything looked fine. We were looking at it at night and didn't notice any sparking or anything, but then i wasnt really looking for it either. Anyways, the next day it wasnt raining and after driving it for about 40-50 miles everything went back to normal. Then the following day it rained again and its been sputtering when accelerating and idling again It hasn't rained currently for a few days but its still doing it and service engine soon light still on and blinking sporadically but, seems to be getting better and better with every dry day. I've read a million different things on what could be causing this misfire. It's obvious tgat water is getting in somewhere, anybody have any ideas where i should start? I dont know much about cars but am mechanically inclined and can understand and fix what you're talking about, just need to be pointed in the right direction

 

Windshield is probably leaking onto GEM.

 

^agreed

next time it rains / sputters - try throwing some heat up under the dash on the drivers side up above the parking brake lever with a hair dryer - if that helps it will verify the cause as stated in the previous post

 

Can also be bad coils. Friend of mine has had them act up when rain. High Changing solved problem.

Check mode 06 data on scanner and see what cyls misbehaving

 

This. I had this happen as well years back and got the DTC was a cylinder misfire. I replaced all coils with motor craft and it never happened again

 

Well you would also think the OP would've had the codes read to tell him what was acting up but here we are shooting in the dark lol

Also when the CEL is blinking... that's a sign to stop driving it until you fix the problem ... but I'm just some guy on the internet

 

Ditto with fordguy2100.
When I bought mine, it had been sitting outside for 5 years. After I finished the motor work, I replaced the windshield. For about a month after that I had buzzers & lights going off at will.
Only after time (and cranking the heater on the floor setting) did it resume back to normal operations.
If you have a sunroof start there then go to the windshield.

 

I'm betting that the engine's back 2 cylinders (4 & 8) are wet from the hood dripping on them The GEM is a body control module, not an engine management controller. Check the codes. Probably a P0304, P0308 and P0316 are there. That's my guess.

 

03's would have COP's huh?

 

Yes sir. All 5.4's have COPS. Also, If the rubber upper weatherstrip strip is gone they really drip bad on the back of the engine and the power panel box on the right firewall.