I’m having the same problem you are having. I’m about 2 months into the protocol and aside from occasional die off, the majority of my symptoms have improved tremendously, but my stomach is in constant turmoil! I had a lot of symptoms, so even though the issue with my stomach is huge, I still feel much better.
I constantly have a distended belly (I look and feel 6 months pregnant). It is hard to breath because my stomach gets so distended and I’m always fighting severe constipation. I’m taking all of the supplements suggested on the protocol in addition to the following for my gut: Betaine HCL, Slippery Elm, Bentonite Clay, Glutamine, a huge dose of mag ox, a cup of Aloe Vera Juice 3 times a day now, and I drink coconut oil and olive oil several times a day. I drink warm water in the morning, and after I take the Slippery Elm (4 times/day), and gobs and gobs of water throughout the day!
I’m sorry I don’t have the answer, but from what I’ve been reading it might take months for this to improve. Maybe someone will see this and have some suggestions for us!