Should I just go ahead with a full repaint?

If you weren't already planning to repaint the car, AND you intend to install a new vinyl top, then I would consider them two separate jobs. You can remove the top trim, and tape off the new top when repaint time comes.

If you are replacing the top, I might consider using POR15 after totally grinding away all rust, redoing the lead seams, and replacing any perforated metal. I'm not sure how well the adhesive will stick to POR15, though. Hopefully those more knowledgable will chime in. If that's not feasible, I'd say use Rust Mort on the prepared bare metal per directions, then prime and paint.

Disclaimer - I've not done this myself. I'm just passing on stuff I've learned from great people here (AdamR, among others) and elsewhere as I research for my own car.

Edit: Almost forgot, but if you are not going with a new vinyl top, then yeah, paint the car. I'd think if that were the case, you wouldn't be asking, though.