another area to look at is the roof- the black trim above the tailgate is held on by a galvanized piece of steel, the steel is screwed inplace, i found that the piece if steel had corroded to exess, and allowed water to run in through the screw holes,
to fix i removed the steel, filled the holes and reatached the black trim using clear silicone sealant, that was 4 years ago and it hasnt leaked since,