Regarding your rust problem, I've used a product by SEM called Rust Seal 39308 for some years now and really like the results. This particular Rust Seal doesn't need anything else once it's dry. You can paint or "Bondo" right over it and it says so on the container.

If you used any of these type sealers, don't put any remaining sealant back in the original container once you're finished, it'll ruin all the container contents.

Follow the dry time recommendations and apply two coats.

Any good auto paint store should carry it.
Ben