Mike, I had a similar situation with my 55 chevy. The roof was the biggest problem. ANY rust that is allowed to remain will come back to haunt you. I have heard a million claims of all sorts of products that will convert rust, encapsulate rust, blah blah blah. The only 100 percent sure way is to get rid if it. My solution was a spot blaster, a bag of aluminum oxide media and a LOT of patience. I had my body on a rotisserie which made it easier. I blasted those pitted areas an inch at a time and as I completed a section I used a wash coat of acid etch primer out of a spray can to hold the metal from flash rust. That will all be sanded off later when it's time to skim coat the area with filler. The acid etch will remain in the pits and seal them under the new filler/primer/sealer/paint. I used one of those harbor freight cheapy spot blasters. The aluminum oxide cost me more than the blaster but it worked great. There you have my two cents! Hope it helps.