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.

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.

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.