Well I was going to suggest krylons new formulated Rust Prevention
spray.. I'm very surprise at how well this stuff has been working for me.. But in your case.. you seem to have a bit more involved.. Thou I have seen guys/gals take body armor and simply cover it up.. Your looking at new body parts..(if the rust is all the way through) is not surface preparations is required.. sanding or even acid dipping, priming and then several coats of pain or just leave it primed.. again just depends on which direction your planing on going.. cheapest or all out restoration.
DO NOT USE BONDO