1st: I'd talk to someone who does body work, they can tell you things that are way beyond my experience levels.

2nd: You are definitely going to have to kill the rust. Go to a hardware store and get some "No-Mo" pre wash, that kills the rust. Then you can put on a couple coats of primer.

3rd: I THINK you'd need some fiberglass cloth to place over the gaps and then work the bondo into and over it. Sand that down as smoothly as you can and then add a couple of coats of primer over it. Then when that has cured, put about 3 coats of matching top coats of auto paint.

That's about the extreme limit of my knowledge.