Sounds like you have the same problem I do with my roof. Mine rusted through above the windshield because mice built a nest between the inner & outer roof panels and after years of mouse urine on the metal it rotted out.
I am going to drill out the spot welds along the roof eyebrow, cut the inner roof header off and splice the header in between the left & right windshield posts. I am going to panel bond the outer roof to the inner on the eyebrow and then weld the inner panel inside the cab. That way the roof won't get distorted from welding and I can do it in a lot less time without all those spot welds.
I bought an excellent used roof assembly from JIMBO59CHEV to do the repair with. The only other way would be buy the inner roof panel and splice it. They are about $200 I think, from American Classic Truck.

1957 Chevrolet 1/2-ton Stepside LB in the Gallery
My Photobucket shots

The person who has nothing for which he is willing to fight, nothing which is more important than his own personal safety, is a miserable creature and has no chance of being free unless made and kept so by the exertions of better men than himself." - John Stuart Mill (1806 - 1873)