Interesting. I do have a autoimmune issue as well (Hashimoto's thyroiditis), but I have never had any symptoms really (besides EC which I don't know is related to it at all).
I do have some allergies as well (had patch testing done a few years ago as well), especially hay fever.
How long did it take for you to notice that there was improvement after you stopped eating gluten? I started last night, unfortunately I still have EC ;-))