I would think honestly replacing as many bolts as you can is your best bet. Other than that I would have them chemical stripped and maybe there is some type of clear rust free coating you can put on the heads without changing the treads size/depth.
Honestly though by looking at your motor(no offense) you should worry about other stuff before the bolts. I.E. Powdercoat your intake mani. Have your alt. cage polished/powdercoated. Take a buffing wheel/polish your radiator. Repaint your coolant overflow tray. And a alternator cover would clean up the bay alot. I think once you did that stuff they start to focus on replcing/finishing the bolts