Any holes through medal should have the souronding area cut out and replaced. Small bubbles will have pitting under them . You`ll not know when you sand them down.It is important to get all of the rust removed or it will just come back. On pitted areas i have used a sand blaster/ media blaster to take away the surface rust. When you are down to bare metal it should be wiped clean with a solvent and primered, until you go to the body shop. Not being able to see your rust , you will have to depend on the body shop guy to help you make the call on replacements.
Contact the Halloween king on the site. He seems to the the go to guy here for body and paint.Besides he likes his chev engines orange and black. (true Harley colors)
Hope this is a starting point for you. Keep us informed will ya?
Slider in Wa.