Roger,
Having owned 2 Sport Tracs, as well as the inventor and manufacturer of the LeverLift and EZlift tonneau cover lift-assist system,I have a lot of experience with the OEM hard tonneau cover.
Originally Ford advertised the cover as being weather proof. When people complained to the dealers that their cover leaked, Ford claimed that the cover was not designed to be waterproof..??? Perhaps not waterproof, but weather proof means it should keep out the rain under normal conditions, or Ford spent a lot of money designed a cover with a lot of weatherstipping for now good reason.
Assuming you have inspected your tonneau cover for cracks, warping or twisting, and all your weatherstripping is in tact and in good condition, there are two possible areas that can cause water leaks. One is around the parimeter weatherstripping, and the second is through the hinge.
The hinge is the biggest suspect since they have actually installed the hinge seal in wrong on some tonneau covers which causes them to leak. The cure for that is to drill out all the rivets in the center hinge, remove the hinge seal and reinstall the seal using black silicone sealant and screws to replace the rivets. This was done by a member named Phill Roccle of NY City. He did a project on this, but I don't know if it's still there.
In my library, there is a document on how to align and adjust your tonneau cover if you have a LeverLift, or EZLift tonneau cover lift-assist kit, but the same principles apply to the tonneau cover even without the lift-assist kits.
Pay particular attention to the center hinge area since that is where most leaks occur. The problem is that the center hold down pin brackets are installed very loosely and allow the cover to bounce up and down as much as 1/4 inch or more. If you ajust the cneter hold down pin brackets to hold the cover down tighter you will probably eliminate most if not all of your leaking problem.
The corner latch brackets have very little adjustment, and as long as the latches are good they are probably OK. If you do need to adjust the latches, you can use a small rotory grinder to elongate the bolt holes in the bracket to give you a bit more adjustmet. I found that just grinding one hole a little longer, I could pivot the bracket downward just enought to get a much snugger fit at all four corners.
Good luck,
...Rich
