I was considering posting more, but things got out of hand. So I'll stick my neck out now.
The bypass door has warped, i don't think there's a good fix except for what he's done, bolting it shut. I don't know if the dealer sold as is or not, with it being older when sold. I don't know the story there.
The brick in the bottom has a gap around the top. The new ones do too, maybe a little narrower than what his picture shows but definitely not tight to the top. I can see a larger gap adding maybe a hundred degrees to the stack temps, but I'm wondering if some of the high stack temps he measured are with the smoke bypass leaking by.
The rough looking metal. I appears to me it goes past some welds, so I would think something really corrosive was in the firebox at some point rather than bad metal. The only thing I've seen flake up 409 SS was some salt water from a pool exchanger that leaked into the water jacket, but that was from the inside out. In this case I don't know and there's no way to go back and inspect it before it was burned, which was why I suggested seeing if he could trade it in.