It sounds to me like you're probably just oxidizing the thrush and whatever other germs you have on your tongue and in your stomach. If the reaction is TOO uncomfortable you could try temporarily cutting back the dose a bit. However, the best thing you can do is just to tolerate the reactions - eventually, the infections should go away...
Personally, I never had any reactions like these (stomach cramps or a brown tongue), but then again I didn't have thrush or a stomach infection...
Another helpful remedy for thrush, candida, and other stomach and intestinal infections is to get a bottle of apple cider vinegar, put lots of chopped-up garlic into it, and let it soak for 1-3 days, and then take 1-2 tablespoons of this in a cup of water on an empty stomach. This is probably just as effective as peroxide (for stomach and intestinal infections at least), but without as many side-effects.