That said, it's pretty clear there's something funky immune going on - the IgA thing, the initial response to Vitamin D (and I second or third the recommendation to get sunlight - go for a walk every day; it'll do you general good anyway). You've got some weird digestive stuff going on, and so my personal red flag goes up, which is intestinal flora.
(Note also: tracking this stuff down is going to be a personal struggle, it'll take years, and there is a truly immense amount of bullshit in the world, so take nothing I say, or anybody else, without a large helping of skepticism.)
My daughter has Crohn's Disease and my son has minimal change disease (a kidney inflammation). After my daughter was hospitalized, we did a lot of research and found out what amazingly bad things can happen as a result of poorly managed intestinal ecology, and after making changes to our diet - some of them pretty profound - she's been symptom-free for three years, our son is improving, and I've lost weight as well.
So here's what I recommend: go to your pharmacy and purchase some sachets of "VSL #3", a probiotic mix. Don't follow the instructions on it; use it as yogurt starter. Yogurt is dead easy to make; get one half-gallon of organic whole milk, one quart of organic half-and-half creamer, mix a cup of plain Dannon yogurt and one sachet of VSL #3 into them as a starter, put it into a gallon glass jar (available from Walmart) and put the whole thing onto a candle warmer for 24 hours wrapped in a towel.
After 24 hours, you'll have three quarts of the most electrically sour yogurt you've ever tasted. Eat that twice a day for a while. If you want to get serious about this cure, take a couple of weeks and don't eat any complex carbs (that's way harder than it sounds). If you've really got an intestinal flora imbalance (you're presumably American, so you do, trust me) and if that's your root cause, you'll feel better in a week. You'll probably feel somewhat better in a week anyway, but there might be more going on.
That's my two bits. I applaud your effort to take your health in your own hands, and if there's anything I can help with, get in touch (email's in my profile).