I can't give you any definitive answers, but do have a story slightly in common. My little girl had a newborn screening test that showed she was heterozygous for deltaF508. Her sweat test was negative and we were told she was just a carrier of cystic fibrosis. Since birth, she has had a raft of digestive problems: reflux, bloating, constipation when she started solid foods, constant gas, and colicky pains after eating. She has always been interested in food but does not seem to be able to eat much at once; now her appetite is not so good. When she started solid foods at six months she became very constipated. In the six months following that, she went from the 50th percentile to below the 1st percentile for weight, and was diagnosed with failure to thrive. She is now in hospital. Because tests have not showed anything remarkable, the doctors are tending to think that her poor weight gain is due to behavioural issues/social issues and possibly reflux. I asked them if they could explain why she was always gassy with a distended abdomen, and they said they would do a stool test for reducing substances. I think this can pick up the presence of undigested sugars, such as lactose- you may well have already had it done.
I hope you get some answers soon. A gastroenterologist would be the person to ask about digestive stuff. I don't know if you've already pursued this line, but it might also be worth having an ultrasound to check that your reproductive system isn't contributing to the bloating with endometriosis or cysts.