Depends where the rust is located. When I tore mine down, the rust was mostly located on the center bar assy, with a little on the top of the windshield frame. I cut out the tiny hole to the size of silver dollar and welded a plate. For the center bar, called Brian at GBody and bought a used one and had it powdercoated. Clean all the rubber and dirt, ospho any surface rust, and paint before replacing trim and weatherstripping.
Carl