Bumping this to throw up my rookie mistake involving water ingestion this weekend.
Apparently the stock air box isn't as water inhibiting as you guys are believing. I went to a spot this weekend with the girl and was bombing through some water holes (water up to maybe the bottom lug nuts, side steps at most) and definitely ingested some water. Service Stabilitrak, Service Engine Soon, Hill Descent, all the idiot lights came on and the truck putted to a stop up at a flat spot. I didn't initially know what happened until I pulled the intake half off and saw a good 2 inches of water in the bottom of the box. I then spent the next 2 hours tearing the intake off, pulling plugs and doing my best to get water out of everything. The intake silencer thing(right in front of the throttlebody) spewed about half a gallon of water when I undid all the tubing and shook it out. There was another guy there with quads and bikes and once I was trying to start the truck, he said he watched a pint of water fly out my exhaust.
Luckily, nothing is wrong with the truck. I should probably change my oil but I was more concerned about hydrolocking a 6300mi engine at the time.
There's definitely a design oversight with the stock airbox as well. The fender tube has a direct line of sight to the intake tube to the throttle body with no baffling to prevent water getting sucked directly into the intake. I'm not saying this is all of Ford's fault as I was the one bombing through the puddles but as a truck that has offroading in mind, you'd think there'd be some form of baffling in the stock intake box to prevent this.
I'll chalk it up as a lesson learned and maybe I'll fab something up for my truck to at least redirect the water away from immediately going into the intake.