I also have kidney pain upon waking, if that helps?
Well, without knowing the relevant clinical details or a detailed clinical evaluation it would be difficult to comment specifically on the situation. Renal anomalies could be responsible for decreased or deranged renal function and may lead to renal failure. One working kidney is enough for normal functions of the body. It would be difficult to comment if your other symptoms could be related. I would suggest discussing the situation and the suggested management plan in detail with your treating nephrologist.
Hope this is helpful.