I agree strongly with the suggestion of making sure you are rested. While I don't have Lupus, a couple of years ago, I thought I might have it. It seems that I probably have Fibromyalgia, with a slightly strange presentation, but I do have some weird genetic markers for autoimmune disease, particularly, colitis, which runs in my family.
I find it's a fine line between exercise making me feel better and making me feel worse. My problem is that I don't necessarily want to "slow down, go easier, do less." My rheumo. once told me to "ride 5 miles..." This from a guy who likes to ride around town in his bathing suit, no shirt, on his old Raleigh with cages on it! I do pay attention to how I feel before a ride or run. My speed is slower, overall, but this year, I rode my most, ever (3,200 miles +).
I now see a pattern. I train for some goal, usually a tour in the beginning of the season. Whenever that is over, it's like my body has done too much and I start getting symptoms, or feeling bad. Late summer/early fall seems to be the time this happens. I'm not going to stop, but I do have to pay attention more.