Repairing a Bondo repair

Judging by the responses I’m getting, sounds like the only way to properly approach this would be to get the entire car down to bare metal and start over?

It's impossible for us to tell from a few pictures. But if the kind of work they did at the roof/quarter seam is indicative of the work they did everywhere else, then the only way to be completely sure is to take it completely back to metal. If there's rust through where you've shown in the pictures, there's very likely rust through in other places. And since they covered it up once, you can probably bet that's what they did everywhere else.

But like I said, a couple of pictures on the internet don't exactly give us a complete view of what you have going on. My concern would be that what you see at the roof seam is just the tip of the iceberg.

It would be very difficult to repair just that area as the vinyl top trim that goes on the car is too close to the problem area.

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I agree, the damage shown from underneath looks like it's about where the trim would sit. Which means repairing it will get out into metal that won't be covered by the vinyl top.

How do you think I should go about this? The car originally had a vinyl top, so I suspect the holes for the trim exist somewhere under there.

The holes for the trim probably exist right in the middle of the much larger rust hole that has now been filled with bondo, based on your picture of the backside of the panel.

And I have to be honest here, I would never put a vinyl top on one of these cars. Or anything for that matter. If you do, it basically means the car must be stored indoors and not driven in the rain. Even humid climates are tough. Vinyl tops breed rust. That's probably why the rust was there to begin with. Yes, you can paint underneath the vinyl and that will hold up better than it did from the factory, but eventually it'll just rust. If you've got a show car that'll never see rain and you can wash and dry it very carefully every time, do what you want. I use my cars as my daily transportation, so a vinyl top is a no go. My bronze GT would be a perfect rust free California car had it not sat outside with a vinyl top before I got it. It needs a complete roof skin replacement and then some, all because of a vinyl top.