Not too sure if this would help, but I had a similar problem with my old 1989 Bronco II before I traded it in. I thought the floor board or something was rusted and got punctured by debris. BUT, when I looked all around, what it was, was a cracked fire wall. Whenever it rained, the water would run down inside the engine compartment (due to the manufactured air holes for the engine cooling process) and followed a path to the front fire wall. Overtime, found a crack and constantly got the floor soaking wet. But that was an old car, and I was dealing with that problem in 2000. Since yours is a newer model, not too sure if that would be it or not.
H. McCartney, December 2004