Rob--my daughter, whom I have written about on this site many times, is taking a natural supplement treatment for a bacterial infection (as opposed to MS meds.) So far, she has done really well.
There is an organization headed up by "real" doctors who believe in LD and the chronic, long-term effects. I no longer have the name, but if you search "Lyme Disease organizations" it will be there. Anyway, they do have a section that lists what are termed Lyme Literate Doctors. I don't know what part of the country you live in but you should be able to find one. Also, I believe almost all states have a LD organization. If we have one here in South Carolina then I KNOW they have to be everywhere! (We are accused of being a little behind the times here in the deep south!) Anyway, they have wonderfully valuable information.
Going to a "conventional" doctor may not help. They only believe in 6 weeks of antibiotics, max. I really like the "natural" approach my daughter is taking as it is less severe and of course has zero negative side effects.
I wish you the VERY BEST!!!