Should I just go ahead with a full repaint?

Many swear by POR-15, but pricey ($40/qt). It degrades in sunlight so top-coat for when your new vinyl gets cracks. I have used Rust Destroyer, which is half the price. It claims to convert rust, etch shiny steel, and good to 800 F. Used to be at Ace, but I had to go to a paint shop to find quarts last time. Also comes in a spray can.

If you do any repair with Bondo or fiberglass, prime the metal first. I understand that water can wick thru them to attack bare metal. I suspect many Bondo patches fail because people apply it to bare metal. I bet weld repairs are almost as bad if all bare metal isn't painted, including the backside of patches.