Interesting Shawn. Sounds a lot like what happened to me back in 1986. I caught HSV2 and had a rash, thought it was over then it came back in monthly-ish cycles and my brain started to get weird, as you describe and more and its stayed that way ever since. Its been a hell of a job just to stay sane. I was undiagnosed for ten years.
Autoimmune responses make a lot of sense, but clarity regarding cause and effect eludes me, in that autoimmune causes for brain problems are a fit but I dont know if that would explain the chronic immune failure, recurring viruses of several different types piggy backing on the problem and TH2 shift symptoms of very severe allergies which I also experience. Its a bit of a conundrum.
But I will return to read more and think about it and am very interested to know how you get on.
Good luck