How to tackle this?

If there is bubbling under the vinyl top it has rust, So, if you want to keep the car remove it and have the rust repaired. I'm not a big fan of vinyl tops myself. I would leave it off and repaint the entire car. I don't know what you budget is for the car. repair as much rust as you can and shoot some paint on it to keep it from re-rusting. Find a car buddy or car club and get a place to work on it. Learn to do as much as you can your self and you can save some $$.