You shouldnt have to paint any outside structure if you weld to the inner structure. I welded to the existing inner fender well. Just don't weld to the lip of the quarter panel. You could use panel adhesive on the lip and clamp it over night. If at a later time you decide to paint you can always go back and weld to the quarter panel lip. But the panel adhesive will hold up fine.Wow.... you had rust exactly in the same places. Thanks for the pictures.If your not wanting to replace the whole pieces, do as you said and cut out what is bad and patch it in. I wouldn't worry about butt welding those areas to make an invisible repair. Cut out the bad spots and make your patch1/2"-3/4" bigger than the hole. Punch some holes in the patch so you can spot weld it around the perimeter. finish them off with body seam sealer and some undercoating. Shouldn't be too bad of a repair. You got this!! The floor pans turned out great so this will be easy peasey for you! Good luck and keep us posted. Also if you don't want to make the patches yourself, you can do what I did and buy the out wheel housing and cut the part off you need. It saves a ton of time and fits great.
I will guess is common. The design of that area is the perfect moisture trap so I am not surprised they commonly rust.
In my case I dont want to touch the exterior painted areas. Painting the car is not in my inmediate or medium term plans.
1971 M-code Mach 1