So when I bought my van, 2000 b1500, there was a rusty patch in the rear passenger side corner under the tail light. I figured either related to the tail light or to the holes someone left in the back from screwing a padlock latch to it to lock the full size door (not sure why since the lock works).

Anyway, the rain is back and water has started pooling back there. I was wrong about where it was coming from though. It was coming from a big gob of seam sealer on the floor at the seam. I haven't been able to figure out where the water is entering though.

As I have inspected things I have grown curious about what this thing is that is mounted on top of the sliding door rail cover. Not painted. Doesn't look stock. One bolt seems to be missing a neoprene/rubber washer which is suspicious.

Thoughts?

 

No, I don't think that is stock. If it is screwed into the roof, that is likely where at least one of your leaks is coming from. If there isn't anything that attaches to that, take it off, fill the holes, see if the leak stops.