Remove all the rust and scale you can. If you have access to a media blaster, even a siphon one using a bucket to hold the "Black Beauty" will do, DO NOT USE SAND !!! Use a mask, even with BB.
Blast away any loose stuff you can find, treat the exposed metal with something like Zero Rust or POR-15, I prefer ZR, enviromentally friendlier, especially to person using it and it does not have to be top coated.I have had better results with it than POR
Feather it in to the surrounding areas, give it a few thin coats, about 2-3 mils each. I would spray everything with bedliner when done. Mask off what you don't want covered and remove any tape BEFORE the liner dries.
Being as you are in "Bean Town" I would take a look under the "cancer carpet" (Dana Farber can't help this kind), you will in all likely hood find rust under there, repeat the process on the interior too. If blasting make sure you cover places like the dash, you'll be blowing BB out of your ductwork for years...lol, trust me ..I know.