I'm having severe right flank pain normal urine, blood, and CT per the er. I have lupus. What could it be? It doesn't feel muscular.

Need to see your MD. It could be lupus nephritis, or even more serious vascular thrombosis must see your doctor with out delay some times kidney biopsy is required.
Possible plerisy. Lupus has been associated with pleural inflammation ie pleyrisy, pleural effusion and atelectasis that decreases lung inflation volume and can cause significant pain.