Have you checked the rear triangle alignment (string test)? One of your photos shows the stay cap is not flat, but twisted which would indicate a possible bent seat stay that twisted the cap out of alignment? I had a similar issue with a Super Course. The stay caps are not attached very well at the factory as they are really just cosmetic. Mine were slightly cracked, but came loose when I was aligning the the frame. I had a friend re-braze the caps, and added a little more brass to the main stay/seat tube joint. The repair left a pretty big gob of brass that took quite awhile to file and sand smooth.

After checking the alignment, If you file most of the brass off, and there is cracks showing at the cap joint, you could just use JB weld to fill the gaps, and smooth the area. Re-brazing is probably not necessary if the main joint is intact. I stripped my frame with Aircraft paint stripper. I then media blasted the frame with Garnet, followed by sanding with 180 grit sand screen ripped into narrow strips.