WOW! First you shouldn't have water at the rub rail, so it shouldn't leak there. I would check the transom and floor if you had any leaks before you put a lot of work into it. pull the rub rail and clean whatever is there up. Don't use 5200. That is FOREVER and you will be screwed if you want to take it apart in the future. I can't think of a reason to "calk" the rub rail, bet a small bead of silicone couldn't hurt. If the boat has been painted keep in mind Acetone is "fingernail polish remover" it will take enamel paint right off, and like Ross says can go POOF with a spark. Don't be afraid to take it apart, it will go back together..