1. Mine were galvanized. If you media blast you will lose that plating so sealing the car is a must.

2. I would tackle one at a time so that you don't over weaken the body. My 2 cents would be to do the floor first, then the inner & outer wheel wells. The rear trunk gutter and quarter adjoin on the bracing which is welded to the inner rocker, once you cut that out you will need to be sure you've braced that area to get the alignment right before putting the new ones in.

I also had to patch the inner wheel wells where the convertible back seat frame was welded but you are replacing those.