If you've been on a high protein diet for a lengthy period of time you might want to consider going (nobody beat my ass up here, okay) vegetarian for about a week or two, just non processed whole grains, lots of veggies both steamed and fresh and lots of fresh fruit. Your body might need sort of a detox, get in live enzymes and living vitamins and minerals. The digestive enzymes and probiotics are also a terrific idea either way. One particular probiotic that I found that helps in that department a LOT is very expensive but has worked practical miracles is Primal Defense by Garden of Life, you need to be taking about six a day for it to really kick in. If you can't swing the $55 a bottle for PD then at least get a probiotic blend.
Last resort, activated charcoal tablets/capsules available at any health food store. You want to take them on an empty stomach, not WITH any food.