Our daughter had c-diff. It went undiagosed longer than it should have. Before we received the results, they recommended Flagyl because it is the recommended first line of treatment for both c-diff and bacterial overgrowth.
with c-diff, our daughter was pooping 10x/day and the smell is really, really terrible. what you are describing does not sound like c-diff to me, especially with the issues of constipation and poor appetite. My little one never ate better when she had c-diff, the poor thing was trying to keep up with all the output!
even after she tested neg for c-diff (following two courses of Flagyl back to back) her gut took all of 6 months to recover...
also as a side note...she recently went on antibitotics for a cough and her poop never looked and smelled better which got us thinking about bacterial overgrowth too. we asked about treating bacterial overgrowth at clinic and they explained they usually treat it with a 3 day course of antibiotics 1x/month and they use an antibitotic that stays in the gut (i.e. one that they would not typically use to treat a pulmonary exacerbation)
good luck
ps how about dairy or gluten allergy?