Yep not as bad as it could be. Roof looks ok and hasnt eaten into the sunroof hole too much. You may be better off using an orbital sander at a lower speed to take the paint off - this will ensure you dont warp it. Re the bonnet, the flap wheels wont get rid of pitted metal, you have a couple of options for this, either you can cut out rusty sections and weld new ones in, get it acid dipped, or ask a blaster to blast it carefully.
With the hanging panels, you wont need to treat these so long as they are under cover as they will need blasting anyway. Try to concentrate on one section at a time, now you have got the bonnet in bare metal, try to finish this off as rust will start attacking it from day one.
With the bolt in the fender, you can try screw extractors, these dont always work and sometimes just butcher what is left of the bolt, or you can drill it out and retap it.
Good luck with it