I don't know what, if any, methylation defects I have as I haven't had the genetic testing. I do have great difficulty detoxing based on feeling toxic much of the time and getting little relief from detox methods. I also have to go low and slow with the herbs.
I have noticed some changes lately. I was on Augmentin for a week in December for a sinus infection. Afterward I had a long two month herx or flare. However, since taking that abx, I've consistently had little to no head symptoms like I had before, even when experimenting with increased doses of antimicrobial herbs that previously did elicit head symptoms. I strongly suspect the abx killed some stuff in my brain/head/CNS and I'm still reaping the benefits. Then, since cleaning up my diet this past week, my whole body inflammation got better and I was able to increase doses even more. Today, however, I felt pretty bad and swollen and sore. Probably too many toxins again. I tend to get overzealous with the doses when I feel less inflamed.
I also learned I am still being exposed to enough mold to affect lab results.
I really think it depends a lot on your total toxic load and your ongoing toxin exposures beyond whatever endotoxins might be released when treating the infections. May very well also depend greatly on how dysfunctional your immune responses are to begin with. I was very sick for 2 years and symptomatic for 7 before getting any kind of treatment. Cytokine remodulating herbs are supposed to correct the altered immune responses, but I've had no change there after 9.5 months.