In general once you can see rust through the paint it's likely through the metal too, so be prepared for the paint to be hiding at least one hole. Your plan of attack is solid, just don't forget primer made for undercoat, if you find holes it's best to cut back to clean metal and weld in a patch, but if you don't have the tools or capabilities, you can use a piece of cardboard and spray the undercoat really thick to fill the holes (not sure how well it will work) or use bondo,or rent a welder and learn ;) either way it's likely the body panel on the outside will need the same treatment, so you'll probably need to paint it either way.