Dear Syd, hi and welcome. Lupus ranges hugely, from mild to severe. So the good news is, it's definitely possible to have it, yet have no permanent damage to major organs (kidneys, heart, lungs, brain). This type of SLE is called "subacute", in contrast to "acute".
Re: your kidney cyst, I have one, too. I was told they're common enough, that mine isn't harming anything (isn't causing any blockage, etc.), and that it has nothing to do with my lupus. But whether YOUR cyst is causing any issues is sure worth asking about & confirming! (I had flank pain, too, but I think mine was related to my chronic bladder misery = burning and frequency.)
If your urinalysis doesn't show protein, and if your BUN and creatinine blood levels are in normal range, I *believe* that suggests your kidneys are filtering properly & are in good shape. But to put your mind at ease, you could ask your doctor or his staff to specify WHICH tests they were alluding to.
Steroids can cause sleeplessness & agitation, even in low doses, I think.
I've been on Plaquenil for 10+ years, and it's helped a lot with pain, fatigue, anemia, urinary & GI problems, hair thinning, migraines, weired neuro problems (numbness & tingling), etc. Even my hair came back to normal, well, more or less, meaning it never was my crowning glory.
Especially in the beginning, reading really helped me tame my worst fears. You could borrow books from your local library.
I'm sorry about your diagnosis---nobody wants this!---but I hope there's some comfort & useful ideas in the above. Also, I hope you keep in touch with us, as you'll meet many nice people who are always glad to chat with you. Sending warm wishes, sincerely, Vee