Hello, A couple of questions...

Like somebody else said, it's not caulk, its seam sealer. You can buy seam sealer in the auto parts store, but I prefer to use Blackjack Roofing tar which is real similar to the factory seam sealer. It's just takes a month or two for it to harden enough 2 top coat.
As far as the floor, I'm not a real fan of the phosphoric acid. I would get in there with a steel brush on a drill and brush the heck out of the floor and then put a rust converter on the floor. Let it cure for a day or two and then coat it with the paint of your choice.