We installed some repair quarters on a 55 wagon (the lower half only) and afterward sent the car for media blasting. One side had so much rust appear that we found an NOS quarter to fix all the damaged areas and cut out the one we just welded in. So with results like that, I would suggest media blast first and then worry about cutting out the rusty areas. If you'll be awhile getting it back together, it wouldn't hurt to go ahead and spray the primer, just don't waste it on areas that will be cut out anyhow....
