I am five days late but am not pregnant, what else coule be wrong? Also my kidneys have been hurting really bad. Are the two issues related?

Probably not related. There is no reason why a delayed period should be related to your kidney. Are you sure that your kidney is hurting? Could it be musculoskeletal? Suggest you see a physician. Kidney ultrasound is the easiest plus non-invasive way of checking out your kidneys.