Do they give you actual numbers, or just "normal"? I'm always more interested in the actual numbers, rather than someone's interpretation of them. (Even when the someone is a trusted expert in their field.)
According to the AARDA, there's no such thing as a test for all autoimmune diseases [1], which is surprising to me. You're probably going to have to submit to a very long series of tests, ruling out one possibility after another, unfortunately. A kind of reverse lottery.
And just FYI, I settled on an autoimmune disease for the following reasons: fatigue (common symptom for a heightened immune response); muscle pain (i.e., flu-like symptoms); numbness / loss of dexterity (nerve damage); nasal congestion (classic immune response).
Medical diagnosis can further be complicated by co-diseases, or other situations where something causes another series of symptoms as an unrelated side effect. i.e., you start with an infection of some kind, which presents a certain set of symptoms, but then you develop a rotten gut as a side-effect of your body's response to the infection, and then you get distracted looking for IBS, and assume that the IBS-like symptoms are causing the rest of the symptoms.
You might try focusing on the possibility of Lyme disease for a while, only because you did test positive for it, and AFAIK it's not a very well understood disease. There are a wide range of symptoms and other problems associated with it, and they can surface years after the initial infection. I think the majority of its effects are incurable but treatable, but I'm not terribly certain about this. The only reason I know anything about it at all is because it's endemic in my area, and there was a possibility that I was infected a few years ago.
Good luck.