unscrew the 3rd brake light and check the rubber gasket, it might be messed up. It's the same light on the F150's and they've leaked around the 3rd brake light too. If that's it, then the dealer should replace it.
This site has all the manuals for the Ford systems: www.gemsen.com/ford
You should be able to buy another fob and program it no problem, check out the silver kit owner's manual for the programming instructions.