cowl

do I need to remove the cowl to get the car media blasted, do the body work and then get it painted?

No, as stated above it is part of the car. To get it blasted remove everything that is bolted, screwed,glued, or somehow stuck to the car. Cut off/out any panel (quarters, corners of windshield etc..) that you know will need to be replaced, so the blaster will get in all the nooks and crannies. See if they offer any more aggressive material (sand) to blast the rust off too.