Would love some advice

At this point, it is best to go down to metal, and fix all issues and go from there. My car was similar to yours in that it had been repainted once, and had the same rust issues. I replaced a whole right rear quarter due to sideswipe damage. the good thing these days is that replacement sheet metal is available that didn't used to be. It is pricey though. In the end, you want a rust free car with minimal filler to straighten the body out.