Sounds like gut dysbiosis, this can lead to acid reflux. Keep away from ppi as you'll never get off them if you start them with dysbiosis. Over time the dysbiosis can travel upwards causing sibo and reflux, this can lead to increase plaque in the mouth. Some people shouldn't take probiotics at all. The problem is we are all unique and we simply don't know which ones suit us individually.
The other problem you have now is that because you have an imbalance, to much of any Antibiotic may make you feel better at first but if you need them long term you don't know how you're going to cope with them.
Also, many people who have tried Antibiotics and think they are cured find that the condition just comes back again.
Truthfully, your gut will improve hugely over time but it won't cure itself. Bacteria is all around us and everytime you place your hand on a surface and put that hand to your mouth you are injesting bacteria, that's good, you need that. Over time things will gradually improve as you injest more bacteria but it's going to take time, I'm thinking a minimum of two years but if you keep taking the herbs that will have an effect on bacteria injested. By this time you will be eating carbs. You will find you can tolerate different carbs than others. For instance you may tolerate the carbs from an avocado but not from a rice cake, it takes time. Many people can't tolerate eggs but that's often not true, it's the whites that usually cause the problem. Rainbow trout is good for calcium intake and is often better tolerated than salmon. Rice bran oil has no carbs. Liquigen is good for fat intake and getting calories higher. Have you tried avocado to see if you can tolerate it, it's usually a very well tolerated food and the carb intake is lower but it is an almost nutritionally complete food. In your case you have to try different foods, you should always start with one tsp.