You are very knowledgeable about the microbiome already as a microbiologist and it seems you have had good success on Visbiome. Your diet sounds really sound, too, so it seems you are doing a lot on the non-medication front to keep yourself healthy. I agree with ScottF that it really good be the stricture that is causing a lot of your problems.
One thing to know about FODMAP is that it is not about cutting out foods, but rather limiting the intake of foods that are causing problems for you. (It is "low" FODMAP, not no FODMAP). I do not want a gassy J pouch, so I try to really decrease intake of foods that may cause a lot of gas for me, whether it is the hydrogen gas of FODMAPs or just regular old gas! The biggest change I have made is to cook with the green parts of scallions or leeks in place of white onions. It still adds an onion flavor to the dish, but eliminates the chance of onions making me gassy. I agree with you that you don't want to get too restrictive on any diet---it takes away a lot of the joy of life. I do eat sugar, drink alcohol, and eat things baked with white flour and it has not been a problem for me. All in moderation!