I get low grade fevers whenever I push my body or emotions beyond a certain point. It's aggrivating because my tolerance for things is not near what it was before diagnosis. Having to take it so incredibly slow aggrivates me more and causes worse problems. What I have to remember (and everybody else) that there is not a lot that is 'normal' about a body with lupus in it.
Your stomach trouble can come from the slightest stress, or that there is inflammation due to lupus attacking your gastro-system. My stools never do what they are supposed to do. The slightest amount of stress and my stomach goes crazy and my intestines pay for my stomach's stress. Everything your stomach has it sends on through to the intestines. Your intestines can only take so much acid. You may have some veggie allergies that weren't there before because of your lupus changing body defaults.
My remissions last for years at a time with very small symptoms. (scattered joint pain, fevers, fatigue) and those symptoms show up only when I overdo things or get sunburned.
Keep in mind that a flare is not the same as showing symptoms. Your symptoms may just be your body fighting little battles. To know what your signs of a true flare are, keep a journal of your symptoms and you'll see a rise of one thing or another that gives you an idea. Do this until you find recurring symptoms that show up without fail before a big flare. Even 'normal' people have aches, pains and little fevers. This is normal activity of your body being alive. See? You're still normal in some places
Pain in your limbs accompanied by fever is due most likely to a fever above 99F. Unlike children who can have a fever of 103 before you get excited, adults can't handle fevers as well. Be sure to do what you can to keep fevers to a dull roar.