Jolon,
I also have looked at the Marshall Protocol and am also quite unsure about it.It is great that it is helping some people who previously couldn't get relief but I am concerned about the long term effects of using antibiotics and other pharmaceutical drugs.
If you remove the source of your problem the body has an amazing ability to heal itself given the right resources. Autoimmune is a huge part of what a lot of us have but people do recover by chelating, eating a healthy diet, and taking the appropriate supplements etc and BELIEVING THEY WILL GET BETTER. I have recently met a lady who was confined to a wheelchair she was so bad and now is nearly back to her old self. Look at Russ and Laura also.

Tracy, I can't believe your Drs! They must be mercury poisoned (ie mad as a hatter!) Ask them to test your antibodies in a blood test. That will show to the satisfaction of the medical profession if there is an autoimmune response happening.