Go to your friendly Ford dealer and buy a bottle of a/c system deodorizer. You can pull your blower motor out in 2 minutes and reach up in the housing and squirt the deodorizer on the evaporator core. You wait like 15 minutes then run your a/c for like 15 minutes with the windows down and you not in the car. It kills the mildew and leaves a fresh scent for your pleasure.
one more thing, look under your car and make sure your evaporator drain is working and the water is dripping out like it's supposed to.