I agree with CTBarrister. When I was taking flagyl, I did much better on the lower dose - 250mg 2x per day rather than the 400mg 3x per day I was initially prescribed. I also did better when I took flagyl alone and not combined with cipro - the two-punch combination of cipro and flagyl completely zonked me out. Cipro also makes me terribly constipated; that being said, most people do tolerate cipro better than flagyl. I'm not in the norm in that respect. As for what you can do right now, I would suggest calling your doctor and seeing if a different dosing schedule for the flagyl or lower dose would be reasonable for you. This may help mitigate the side effects. Alternatively, adding cipro and halving the dose of flayl may also be an option - see what your doctor thinks.
That being said, I do try to avoid antibiotics at all costs, since the side effects are often worse for me than mild pouchitis. I have to be in dire straights to even consider them these days. Unless I have a raging case of pouchitis (which I've thankfully only had twice), I always feel better off antibiotics than on. They mess up my system for weeks. I'm lucky not to suffer with chronic pouchitis, however. My surgeon agrees with me that we should try to manage the mild inflammation "sub-clinical pouchitis" with probiotics as a first line. I do take align, and have had reasonably good results with it for about a year now. Once you get off this course of antibiotics, you might want to start taking probiotics for ongoing maintenance.