Barngurl, your doctor may be partially right in that some of your symptoms may be due to an impacted organ or body part. He is wrong in that two weeks of antibiotics will not "cure" Lyme, even in the early stages.
Lyme and its co-infections affect many parts of the body to the point where your body will be symptomatic of whatever organ it has affected. Lets take MS for example, Magnesium deficiency, which most Lyme infected people suffer from, can do peroxynitrite damage (migraine, multiple sclerosis, glaucoma, Alzheimer's disease) as well as cause hypertension, cardiovascular disease, kidney and liver damage, etc. (http://www.ncbi.nlm.nih.gov/pubmed/11425281)
I was diagnosed with Fibromyalgia when my Lyme tests were negative. I was prescribed SSRI's which would have been useless and I would have suffered needlessly if I had not persevered and had finally found a doctor who could treat me by symptoms alone. I too was finally given Amoxicillin by a doctor later in my quest for a cure and have seen my symptoms slowly go away or lessen in severity.
The range of pathologies associated Lyme can be enough to make any doctor diagnose a patient incorrectly or just partially. I call Lyme the "mother of all infections" because of how it affects the brain, heart, endocrine system, the gastrointestinal system, bones, nervous system, vision, hearing, and walking.
I read somewhere recently that doctors are now treating MS and Rheumatoid Arthritis with antibiotics because more and more evidence is coming to light that people with MS and Rheumatoid Arthritis have a bacterial infection. (http://www.immed.org/illness/autoimmune_illness_research.html).
By the way, I have stopped my antibiotics twice and in both instances, Lyme came back within a few days of stopping the antibiotics. As a matter of fact, only one eye was affected with Lyme and after stopping the antibiotics, the other eye was infected soon thereafter. Now both eyes have Lyme and its effects (floaters, dry eye, eye pain).
Post Edited (Healing98) : 9/20/2013 7:59:03 PM (GMT-6)