lynbrez - goodness - what a journey. Your detox regime looks good. Epsom salt foot or full body baths are really good and I'd highly recommend integrating those. I suffered from headaches terribly as well. It is the treatment that helped things get better. I still get them, but bit by bit, less often.
If your gut is telling you that you need more bacterial killing, and you are off treatment for killing right now, perhaps it would be a good time to test out some herbs and try an herbal approach. From your condition, it sounds like it not be all related to detox issues, but symptoms related to the infection - something else that needs to be hit up. I went the herbal route, so I can't advise much on your treatment. If you haven't had a treatment that kills bacteria in 4 weeks, I doubt this is related to a herx.
With regards to detox herbs: the milk thistle is good for that, for your liver. I found this nice blog post suggesting detox herbs.
http://blog.paleohacks.com/8-herbs-that-detox-your-body-naturally/# I think that your LLMD has you working on your gut is key and a really good direction.
What are you doing for your sleep?
For brain stuff others have recommended Kudzu.
For herbs to kill bacteria: cats claw or Zhang's allicin could be good to start and a good support herb in the herbal route would be Japanese Knotweed.