I don't put that much effort in cleanliness as shown in the first tig weld picture, it was just lightly blasted then welded, all 1956 GM metal. I have parts cars and try to use original metal whenever possible. You might need to look elsewhere for the problems you are having.
All the 1957 quarter panel parts were acid dipped. The lower side of the quarter patch panel was rusted out so I used an old rocker panel for the bottom patch panel, and it was one gage thicker than the quarter panel. The rocker panel was welded on the donor quarter panel before cutting the patch panel out.