I'm glad they figured out you have c.diff as it's nasty. I've had many bouts of it. Before my j-pouch surgeries one occurance was caused by Cipro so I can't take it for pouchitis or anything else. After my surgeries I had a prolonged bout of it. It subsided but only after taking 4-5 courses of of flagyl. If it ever comes back I'm planning on asking for vanco for several reasons including I don't want a 8 month marathon with it again. My GI at Mayo's has me alternating the use of flagyl and augmentin against pouchitis because I can't take cipro. It is considered pouchitis too as are many things. It's my understanding that "pouchitis" means inflammation and there are many reasons our pouches can be inflamed. Dr. Shen co-authored the following and I think it's a good one to read about anything that can go wrong with our pouches.
http://dom.pitt.edu/gi/fellows...eadings/shen2005.pdf.
As Scott mentioned Saccharomyeces Boulardii is a probiotic yeast specifically to fend off c.diff. I order mine on-line but am sure you can find it locally. The kind I've been using includes MOS and is made my Jarrow Formulas. I take one gel cap twice a day and refrigerate it as the label says that might extend it's shelf life. It doesn't come refrigerated like VSL#3DS.