I noticed after a rain that it felt damp in the truck, it went away so I thought it was just humid from raining. Then a week or two later it started to smell musty and moldy. I tried riding with the windows open, sunroof open to dry everything out but still when I'd close up the truck it smelt musty and moldy after that. I then started to look up and down and all around to see what the smell was and I found that when it rains, the sunroof leaks quite a bit and dripped down through the interior. I have an appointment at the ford dealer to check this out later this week.

Update from Oct 23, 2017: The problem was a kink in the Right front sunroof drain line, that was fixed. To mitigate the musty mold smell, they replaced all of the interior fabric, seats, headliner, carpet.... After the fix, when I picked up the truck, it had an extreme dose of deodorizer all through the truck. It was on the overwhelming side. It did disipate but some of the mold smell started to come back. I took the truck back and they had found another subject piece that had mold on it. The firewall material had mold in it. They had fixed that BUT when I picked it up it smelled close to the same as it did, the smell comes and goes depending on the humidity, if I use the A/C or not, possibly the upper or lower vent... Trying to get a response from Ford...