Vinyl top troubles...

You should be able to buy the tool at most local parts stores. I 'think' mine was made by K-D Tool, I've had it so long I'm not sure now. They also make a straight one but I like the 'triangle' type best, too. It's a flat metal tool with a hook on the end. It slides between the rubber and the moulding and the hook pulls the clip away from the moulding so it will release. You kind of rock the tool sideways a little to pull the clip away from the moulding. It's simpler than I can make it sound.
I have used a razor blade scraper on the glue, works well on certain types. Transtar and other manufacturers make 'adhesive remover' which will make it easier to take off, too.
As far as the bondo goes, it looks like a quarter has been replaced as there isn't a seam at that location from the factory.
Good luck,
Dallas
missourimopar.com