Low-carb is killer on gut bacteria, and according to others here it can be a looooong recovery. Probiotics (in live food not just pills) as others have mentioned here can help. The other thing you might find helpful is aloe juice. It really helped me with some stomach issues awhile back, and will make you very regular.
Overall, it just takes time. My stomach had some issues after coming off the pill a few years ago (the pill also harms the flora), but my gut seems pretty good these days.
I also second Tina’s advice for a well-balanced, moderate diet. Our grandparents were onto something.