I'm not familiar with that specific test, but many including myself do not believe eradication is possible in late stage Lyme (at least with current treatment options).
I would not discount EBV as a factor and maybe that can be addressed in some way.. however, for the most part I think you can say you've done enough antimicrobials, and that your treatments would be more worthwhile if they focused on rehabilitation and immune modulation.. probably would have much more success in reducing "neuroinflammation" that way. I guess in the end I kinda agree with your doctor there.
I was one of 2 patients out of the thousands that he's treated that didn't get better when we "should" have
This sounds fishy to me.. I suspect he's given that line to more than 2 patients if he's really treated thousands.