I took my truck into Leer again. This time we did a water test. We found a few things.

1. Tilting front window had plugged or "too small" weep holes in frame causing the frame to leak inward during heavy rain. Dealer drill the weep hole a bit. I will update once we get some good rain.
2. Next we focused on the bed rails and found that water was hitting the bottom of the bed rail trim from road spray. I asked Ford and was advised that most truck do not include the rear fender skirts that would help with this. Since the parts to complete this would be around $150 I chose the more economical route: expanding foam insulation spray from Home Depot.
3. Lastly we found more holes at the front of the bed just under where hte canopy mates to the front bed rail. There is a small hole at either side of the bed front panel where in meets the side panel. Once again I used the expanding foam to plug the holes.

I will update all once I get some time on these fixes.