After looking at a lot of pictures, I'm inclined to think it's candida as well.
It's so strange you mention "little yellow stone things"... I have been getting those too!
I don't think they're undigested food/pills... they're a light yellow that could be mistaken for corn (only I haven't eaten corn since I can remember). Perhaps 1/4-1/2 mm in size,kinda hard, irregularly shaped, with slight color variation/striations.
Maybe it's something to do with the coffee enema in particular?