IgA is immunoglobulin A, which is likely directly related to your nasal congestion. The elevated levels could either be causing the congestion, or a result of the congestion.
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.
[1]: http://www.aarda.org/infocus_article.php?ID=15