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Since they contain probiotics, die-off is a possibility. Another reason is, like you suggest, dairy intolerance. It’s possible you can overcome this by continuing to eat small amounts of lactic acid bacteria (from the yoghurt/kefir) until they pass on useful genes to your indigenous bacteria. Starting any food in large amounts, especially after avoiding it for some time, is generally a bad idea.
As for sugar, Greek yoghurt is the best variety to buy. With kefir, homemade is by far the safest, cheapest and most beneficial kind. Getting the grains is easy enough online, and making the stuff is even easier. Well fermented homemade kefir will probably be less than 2% lactose, and have much more CFUs and a higher number of strains than commerical kinds.
Given your symptoms, 100-200ml or so of homemade kefir per day for 2-weeks could be a good starting point if you want to continue dairy. Then you can try increasing it. You could try the same approach with small amounts of Greek yoghurt or commerical kefir if you like.