Clean the area very well with non clorinated break cleaner, or whatever you feel you need to use, then I would get some “NO SAG” Dicor, or other brand roof sealer you like. If you use self leveling, it will run down the side trying to level itself so it needs to be no sag. Squirt a generous amount inside the hole, then use Eternabond tape with rounded corners and roll it in place to get a good seal (you might let the liquid sealant set up before taping to give you something solid to press the tape against). Then you need to no sag calk the edges of the tape because UV breaks down the adhesive of the tape.
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2002 3280RL, Gen-Y Executive Pin Box, 2009 F-250 6.4 Diesel
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