I fear you may be in trouble.... Lyme disease is an excellent working diagnosis for your symptoms. If a PCR was done as your lab work then a positive test is very specific. But the problem I fear for you is the amount of time that has past. The diagnosis of chronic Lyme disease is in much debate.The term "chronic" may be confused with or interchangeable with the term "late". This means that the treatment for it is also hit or miss. I would stick with your current doctor she seems the better diagnostician.
You are not dying but the disease and the treatments are all going to make you feel lousy. What you need to do is seek out your own interdisciplinary team : Infectious disease, Rheumatology, and Physiatry (PM&R). Use them all to find the best direction for your care.
You also need to inform yourself. Websites such as this are not the place. Go to your hospital's library and start with this article:
Best of luck you have a long and difficult road ahead of you.
If you are Ig-G positive for Borrelia burgdorferi then a PCR test confirms the diagnosis. The treatment for and the success with late term diagnosis is what is so difficult. PM&R doctors are very good with chronic pain syndromes. Some of them do not include this in their practice so you must ask, but they are very good at this.
Also try: http://www.nlm.nih.gov/medlineplus/lymedisease.html#cat5
This site has lots of links.
Thank you for the accept