Cut away the rust and install Bush-wacker or similar flares.
Or locate a used bed.

 

My question would be if you cut away the rust won't the new flare (Bushwcker or Jungle) be too short on the bottom where the flare meets the side molding?? I probably have to cut and inch or 2..

 

You most likely won't know until you have a flare in your hands. You could always add a fiberglass fill panel to attach the flare too. As long as the glass is attached to clean solid metal above the rust. Gonna have to get creative since no-one that I'm aware of make replacement wheel/fender arches.

 

i need to take the wheel arch moldings off my truck for the season still & clean them out, and re-wax the metal behind there for protection but temps are getting nippy and behind schedule yada yada
and salt season is soon to come

 

Sand and cut the rusty metal then apply a zinc filled primer on the bare metal. You can coat both side of the panel for long lasting protection.This is no ordinary primer because it will etch the metal and prevent future rusting.You can do the bodywork when weather permits.

 

I live in NV. This is not an issue for me . But i'd try to cut away as little as possible and sand as much as possible.

 

some might suggest to closely inspect that frame from under, too