This is my first post. I have a 2004 Super Crew. Driving to Phoenix last week we hit heavy showers a few times for short duration. Next day, there was a terrible odor in the cab. It went away after a few minutes (a/c was on). Later in the day, same thing. By second day, no more odor. We had the a/c on almost constant for several days and no odor except after the rain. Thought water got inside door, but no. does anyone have any ideas? Thank you.

 

Do you have a sliding rear window

 

Check your third brake light. My seal was leaking letting water in and was replaced under warranty. Unfortunately I didn't find out in time and I have this awful mildew smell in my truck when it gets really cold or really warm out. Eventually going to rip out the interior.

 

is the carpet wet under your mats ??

 

If you have a water leak (carpet wet by passenger compartment, or behind the seats), your not alone. Its been discussed many times on this forum before. The three most common places for water to enter the cab on these year models are the A/C drain plug (a real PITA to get to) and this one has a Ford TSB for its repair recommendation, the third brake light (on roof), and the large grommet located behind the battery where the large wiring loom enters into the passenger compartment to the fuse box.

If you have no water leak, then the AC ducts may simply need to be deodorized. During the humid months, you should run the AC for about 2 minutes after you park it (and before shutting it off) to clear any moisture that can build up and mildew in the duct work. Most auto stores sell a spray or drops that you can put into the ducts to remove the odor. The vents pull off (place your pointer and middle finger into the vent and pull back). Now spray into the ducts.
If you run the truck and AC for a minute or two after you park it, you can prevent any future moisture/mildew buildup from happening again.