Diarrhea is better than constipation as you are flushing out your system. It's good for you to a point at which you start getting inflammation.
Your doing the right thing by backing off and then starting again at a lower dose. Sounds like it is going to take a while but it will be worth it. It should clear up at least some of your problems and then you can try something else like Iodine (Lugol's).