Hmm, it sounds like you're doing everything I would suggest. I will say, once I was off the Big-3, it was months before I could eat without pain and/or nausea. I managed to get through it all be eating tiny amounts of food every 2 hours, whether I wanted to or not. I often made a pitcher of protein smoothie, filled with whatever fresh fruit/veg I could tolerate as well as juice and kept it in the refrigerator, then poured 4oz at a time & drank it. My daughters cannot have dairy, so they substitute another "milk" for the Greek yoghurt I used. My friend uses goat milk kefir (fermented liquid yoghurt) in her smoothies.
It certainly would seem reasonable to have sputum tests done to determent the severity of your MAC, and whether there are any other infections like pseudomonas. Since your gut issues have persisted so long, have you consulted with a gastroenterologist to try to get a complete diagnosis?
Sue