I would eat lower sugar fruit such as apples, berries, watermelon, etc. I would avoid higher sugar fruit such as pineapples, grapes, and tomatoes, etc. Avoid high mold fruits as well (pineapple and grapes fit the bill). If you can get fresh pineapple (like in hawaii) go for it but the stuff you get at the store is weeks old or more.
http://nutritiondata.self.com/ is a great place to figure out which fruits are low, medium, and high in sugar.
I would try out fermented cod liver oil to reduce inflammation and try some prebiotics as well, such as buckwheat, inulin (FOS), teff, etc. These can feed bad bacteria but hasn’t been a problem for me. I would either take bitters or digestive enzymes which heal leaky gut as well. SF722 is also another supplement that heals leaky gut (not as much as the others). There are a few others such as marshmallow, licorice, etc.
I am unsure about the water kefir causing problems; I guess trial and error would be a good way to find out. Take a break from it and see if you improve faster or not.
I know of a homeopathic that heals leaky gut if you are interested.