*****if the spirochetes were in my head or pituitary gland...would they show on an MRI?*****
Spirochetes are bacteria and although they're one of the largest bacteria------ they can only be seen via microscope-------not on an MRI.
****. I should probably ask the LLMD about this huh?*****
Got THAT right. 
And before you see him, save yourself and him some time by finding out more about these diseases.
A primer for people in your position is, sadly, hard to find. That's partly due to the immense complexity of the bacteria and disease(s).
The closest (that relies on scientific knowledge) is a rather long one by Tom Grier:
The Complexities of Lyme Disease
A Microbiology Tutorial
by
Thomas M. Grier M.Sc.
Lyme Disease is a multi-system disease which can affect virtually every tissue and every organ of the human body.
It is a disease which can be mild to some, and devastating to others. It can cripple and disable, or fog your mind.
It can affect men, woman, and children, and even your family dog. (1-5,7-19) You may test negative for the disease, and still have it, or test positive and be symptom free.
Some will get symptoms within days of a tick bite, while others may have it for years before they are even diagnosed. Some Lyme patients are told they have fibromyalgia, chronic fatigue syndrome, MS, or some other disease of unknown origin. (See abstracts of the 1996 International Lyme Conference)
There are some studies which strongly support that the infection can be transmitted from mother to the unborn fetus, and may even cause still birth and has been implicated in some SIDs deaths. (MacDonald 20,45,52,53)
Why is Lyme disease such a mystery?
Why does it mimic so many other disease?
Why is it so difficult to detect?
The reasons come from the microbiology of the bacteria that causes Lyme Disease.
Lyme disease is caused by a spiral shaped bacterium known as a spirochete. Diseases that are caused by spirochetes are notorious for being relapsing in nature, difficult to detect, and great imitators of other diseases.
Syphilis, Tick-Borne Relapsing Fever, and Leptospirosis are other examples of spirochetal diseases.
Lyme disease is caused by a bacteria called Borrelia burgdorferi, named after the man who isolated it from a Deer Tick in 1981, Dr. Willy Burgdorfer.
The following is a tutorial to help explain away the mysteries of this bacteria, and why it causes so much controversy between patients and the medical community. (1)
Please go to this site
http://www.canlyme.com/tom.html
and read the entire article. (It took me several times before I began to understand)
ONLY an educated (in Lyme disease) patient can begin to understand how complex and serious and difficult to treat Lyme is.
Then----- there are the co-infections. 
"The part of my recovery plan that I would say made up 80% is MDJ. I suffered a lot prior to finding MDJ, felt alone and had no one to talk to who really understood me. In the Bipolar Group I found like minded individuals who I could relate to and who offered support to me when I needed it. As I recovered, I could then offer support to them which gave me a good feeling about myself. I have met some great people here who I would class as good friends and know I would still be in the slump I was in without them. Now I am stable, I know that MDJ plays an important part in keeping me that way. Thank you MDJ for being there for us all and making us no longer feel alone." (liamacker)
It's a mattress cover that warms the bed. Aaghh the little things in life. 
