JB weld pits in floor pan?

I'd lay the new pan over the old one. Trace it out with a sharpie, then cut inside the sharpie marks for the overlap. Change the whole damn thing, pits and all if you have a new pan. Unless you can remove the corrosion out of them completely, a skim coat of JB weld wont hold up for long.
Doing the skim coat over pitted floor pan steel on something you intend to keep if you have a new replacement pan section to replace it is "cheese dicking" it. It will take about the same amount of time to cut it all out and weld in a new pan section as it will playing Johnny fuckaround with a pitted floor, a wire welder, and JB weld.