Also, rplace your whether stripping(Thats the dmn problem!) .
No offense intended, but actually that isn't the problem. There are two types of rust involved in the body, one from moisture dirt and salt. The other is galvonic rust which is a result of electrical current running thru the skin (starts mainly at welds and moves on from there).
There is no way to prevent water from gettting inside the tail gate. It is a good idea though, since the old hard weather stripping contributes to sctatching up the widow. You need to cut out all rust to get rid of it before putting on any new skin. If you don't it will continue to eat away at the tail gate. Once you have the rust cut out, seal the inside with something like POR15 which will seal any surface rust. Make sure the drain holes in the bottom are clear so when water gets in can drain out.
Good luck,
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