I think you nailed the problem. Good job! Looking at the resulting economic stones list again, it does appear that the very soft metals, like gold, tin, etc., that got modded down to a low max_edge, are the ones showing up on the economic stone list.

That's very bizarre. I didn't change kaolinite, and I'm not sure if I actually changed anything in inorganic_stone_mineral.txt at all. It might only be in there accidentally.

Just fired up my copy with my mod in it, and kaolinite isn't listed as an economic stone (though all stones can be used for sharp blades, since I made it so that all stones have a better max_edge; basalt, granite, etc., have been used as axe-heads in prehistoric times after all). Not sure what's causing the problem.