There's definitely a channel between the windshield frame and cowl, so I think windshield water shouldn't be a problem. I'd love to put a GoPro in there, button it all up and hit it with a hose to see just how much water actually collects...Hmmm... my experience is that the cowl sees a ton of water off the windshield when the vehicle is sitting, and in fact, is designed to drain water out each side and down the fender. I fear that in a heavy rain, you may just fill your entire intake with water.
Not so much concerned about taking on water, though it would be nice to know EXACTLY when water becomes a concern. With the stock location you're kind of guessing. The truck is pretty damn tall at this point, between the 5-ish inches of spring lift and 1" body lift.If your rig is anything like mine height wise, the intake would be almost 5 feet height in the engine bay. Are you concerned that you might get that deep in water? Maybe consider running the intake back and drawing air from the rear most opening of the passenger fender?