Body experts. Advice?

I would use RustMort before welding. It is really hard to clean up all areas before welding to bright shiny metal. After the metal is prepped, go ahead and use weld through primer where you ar going to weld epoxy primer everywhere else. Here is a picture of my 71 Barracuda floor board that had quite a bit of surface rust that was prepped with RustMort. After wiping it down to remove the residue, it was ready to prime over.

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Just remember that if you use RustMort or a similar conversion treatment before welding you'll still have to clean the areas you want to weld on back down to bare metal. The oxide it creates doesn't really weld any better than the rust does. Nothing wrong with doing that before you weld, but the places getting spot welds still have to be bare metal and not oxide.