The seal is just a rubber strip that wraps over the hinge. You might be able to order the seal from your local Ford dealer, and I am sure it will be pricey. The alternative is to find a strip of rubber or make one out of an old rubber inner tube or something similar.
You will need to disassemble the hinge by either removing the screws or drilling out the rivets. (early models used rivets, later models used screws). If you have the rivets, you can replace them with screws. You may also want to put some black silicone sealant between the rubber and the tonneau cover so no water gets past the seal.
There have been several members here who have had to fix their hinge seal because it was installed wrong at the factory...so it is very do-able and does not require a lot of special tools or skill....just time and patience
...Rich
