In a nutshell: Candida=lack of b-vitamins (getting worse over time, which would explain why maybe now you are seeing food in your stool)=lack of hydrochloric acid=lack of pancreatic enzyme/bicarbonate output by pancreas=poor digestion. Somewhere in there the liver/bile output gets affected too it seems, but I'm not quite sure where in the chain of events that happens.
I would suggest digestive enzymes (Soloray is one my ND said was best--the one with peppermint in it) and do a trial of HCL to see if you need it (see link). Also--take 1 or 2 yeast free b-complex vits daily, in addition to whatever multi-caps vit you are taking (yeast free too).