Kevin-
My ex J Pouch specialist (who was mentored by Dr. Shen at Cleveland Clinic) told me he thought fecal transplants would be a waste of time, but I had tried VSL#3 DS, Culturelle, Align, and other probiotics cold turkey after going off antibiotics and none came close to working. Antibiotics work well for me to keep the pouchitis in a low level "simmering" state (according to my Doc who described it as "simmering"). I have seen many posters on this board who reject as implausible the idea of being on antibiotics permanently. I am here to tell you as living proof it's doable and I have done it for 20 plus years with some minor side effects here and there. Rotating antibiotics is of PARAMOUNT importance which is why dabbling with a couple and giving up is not the way to go IMHO. The only antibiotic you have used that is effective in treating pouchitis is flagyl. Cipro is a superior antibiotic and broader spectrum but they can be taken together as they are in different antibiotic families and work on different bacteria, giving you the broadest possible "shotgun" coverage.
But who knows maybe fecal transplant will work. How did you respond to other probiotics?