cab corner pocket repair

[forestb]

I was looking down into my cab corner pocket (the hole in the floor directly behind the door) while I was installing some dynomat. both sides were full of dirt and broken glass and an old bolt that looked lit it had a layer of paint on top of it all. I dug it all out and this is what I found. My question is, is there supposed to be seam sealer over the crack and hole I found on one side? That is what I was thinking because the other side seems to have some seam sealer covering it up. Also how should I get rid of the surface rust out of the pocket? I don't think I can get any tools down there.