Rack mounting

Okay so I have a custom built roof rack that at one time was on my jeep. The bolts rusted from being on the coast wand broke off in the brackets they screwed into. After realizing the dimensions are basically perfect to go on the roof of the trailer I plan to build I would very much like to use the rack. Only one problem... How to I mount it without having to worry about leaks of water infiltration. I'd hate to spend the time and money only to ruin it by poorly mounting a roof rack. My roof will be flat with about a 12:1 downwards slope(6 inch drop over approx 6ft). Does anyone have any suggestions as to anchoring that works without compromising the integrity of the water seal?
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