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You probably have gunk in the air intake for the A/C - heater. It's in the cowl above the passenger side wiper blade. Ford makes a mildewcide that eliminates the smell, a lot of detail shops can do the same job for you. Check the drain tube for the A/C underneath the passenger footwell, it may be clogged and that may be contributing to your problem.
Rezvani's Latest Post-Apocalyptic Monster Is a Ford F-150 Raptor Underneath
Slideshow: Called the Fortress, the 850-horsepower pickup combines Raptor underpinnings with military-inspired features, survival equipment, and a starting price of $285,000.