If there is a structural problem involved I'd attend to that first, maybe put in some bracing or whatever to compensate for any weakened metal.
Then I'd get a rust proofing wand spray gun arrangement, one with a flexible wand that enables you to spray into box sections and out of sight crevices. With mine Fishoilene was sprayed into all those sorts of places during the rebuild. You may not have that in the US, its an anti rust penetrating mineral turpentine soluble clear coating that remains tacky for a long time after application. Whatever, you know what I'm getting at, something that goes over rust, neutralises it and prevents further rusting.
While your're at it, spray in the sills/rocker panels etc too, great fun, not