I don't know what to tell you to do except that I'm also struggling with it. I have taken a variety of herbs to keep the parasites and bacteria out of my liver but this is impossible. None of the herbs work 100% and the Antibiotics would create resistance pretty soon too.
Jarrows Bile Acids gave me internal bleeding and severe cramping so I had to stop them.
What I am planning to do is to keep rotating herbs and keep flushing. There is definitely a benefit in regularly flushing the stale bile out so that it can be replenished with fresh one. Also, I am pretty sure that you still have stones plugging you up in the liver, otherwise you wouldn't have severe digestive symptoms. Are you taking anything to soften them up? I've just now bought some tart cherry juice without sugar. It's supposed to have even more malic acid than apple cider. Also, taking Taurine increases bile production.
In terms of herbal dewormer, I find Vaxa Parasitin to work extremely well. The problem is that we get reinfected all the time. The bugs are drawn to the toxic bile and keep eating it, that's why it's so brown.
For healing the small intestine take Okra Pepsin as it attaches itself to the intestines and helps the healing while the pepsin eats away at the crud.
Removing the gallbladder will open up a new can of worms (literally) and pretty soon you would have to deal with serious colon cancer. Supposedly, people without a gallbladder have a 50% risk of colon cancer. Good luck and keep flushing and killing parasites.