Bone broths contain naturally occurring glutamates. For some people these can cause similar reactions as MSG. Whether this is a cleansing reaction is up for debate.
Usually people who take glutamine for gut healing do not experience herx, but in a severely compromised gut any strong healing agent is suspect and you have to be careful.
I don't know how well you tolerate fats, but one thing you can do is to incorporate raw or cooked saturated fats with your fermented foods to lessen the reactions. You might also experiment with small amounts of Bentonite for the same purpose.
Healing the gut is difficult if you go down this road. maybe there are more efficient ways to do it but I never found one.
Just go at your own pace, don't push your adrenals too hard and damage them.
You might be dealing with abnormally difficult cleansing reactions if you have Lyme.