Tex, I have been thinking about this problem, and of course you do not want the boards sitting in water. Because on your truck the front panel is bolted to the front cross sill there is quite a shelf for water and mud to accumulate. Even with a cover, moisture can get in and cause problems. Your drain really needs to be at the bottom of the boards, not at the top.
Another idea you might try, shorten the boards about 1/16" or 1/8" to provide a slight gap at the front bed panel. Then drill your drain holes in the front panel right in the bend where it bends under the front edge of the boards. Probably drill your holes about 5/16" diameter and a few inches in from each side, and be sure to paint the bare metal after drilling. Just be sure to keep the front of the bed clear of dust and mud that would accumulate and stop water from draining out.
GM added similar drain holes in the front panel of 67-72 fleet sides with steel floors. I think they just built wood floors with enough clearance to let the water drain out.
Let us know what solution you use and how it turns out.
Mar-Ktech
