Good work Shroom.
In personally speaking to various ND's and herbalists about IBS, Leaky Gut and Candida symptoms, the biggest commonality I have heard that causes these types of problems is "food is not being digested enough"; this then causes a sequence of events that results in the symptoms from which many of us are suffering. Not to go along completely with this line of thought, but your yeast/fungal tie-in with stomach acid production would make *perfect* sense within this theoretical model.
Also it's said that stomach acidity and intestinal pH are in an adversely proportional relationship. So this would precipitate favorable conditions for anaerobic organisms/fungus/yeast and unfavorable for the 'good guys'. This and lousy processing/absorbtion/assimilation of our food which would explain the b-vitamin deficiency symptoms despite supp of the same, and a generally sound diet.