I have had my truck for 6 months. No issues. One morning I leave to work during a steady rain. I open the door to find about a 1/2 gallon of water in my weathertech liner - drivers side. Water is also dripping from my A-pillar grab handle. I drove to my Ford Dealer and showed the service tech while it was raining where the water was coming out. I couldn't leave truck until two days later. When I took it in, Ford subbed out the work to a company called Water Doctor. Next day Ford called and said all ready and that the water was coming from the door. Faulty weatherstripping channeling water into the truck.
I certainly had doubts about that. I asked about the Moonroof drains and Ford said Water Doctor checked and they were all good. I know they actually did something because I had glue on my paint in a couple of places from the weatherstripping (job) they did. It was not raining then, but the next day we got a big rain. Sure enough when I checked, water a pouring in. Damn I was pissed.
I checked youtube and found a video of removing a headliner and also a F250 schematic of drain tube locations. So I took matters in my own hands. I unscrewed the two screws on the grab handle and lifted it out carefully on the dash as there is a small speaker in the section. I could see the drain tube snaking through the pillar. Next I needed to remove one of the screws on the visor. This allowed me to pull the headliner out enough to see the drain tube connection. The drain tube material is like fuel line (rubber hose) and a connection is located up in the headliner area and is accessible. At first when I opened it all up, I wasn’t sure if it was disconnected or maybe I pulled it apart when I opened up the headliner. I pushed the connection a tight as I could. But then I thought about blowing the line out as it could be clogged. When I reached back in to pull it back apart, it was VERY hard to disconnect. So I knew then that it was actually disconnected and causing my problem. I blew into it and it was not clogged.
The tube was connected enough originally for 6 months before coming loose as I had no water issues prior. I reconnected all back and no water issues at all since. So what I learned was that my drain tube must’ve been barely connected from factory and wiggled loose in 6 months. Also Water Doctor sucks.

 

So, the drain tubes are only for those trucks that have a moonroof?