Flank Pain After Waking Up, Eases With Body Movements And Urination, CT Shows Kidney Stones. Possible Diagnosis?

Hi. I m a 33 year old female w/ history of kidney stones , recurrent uti, and ovarian cysts . I am current on cipro, sprintec, naproxen and hydrocone. Symptoms that I have been having are flank pain( lt side radiating around to my abdomen, abdominal pain, HA, waking in severe pain after several hours of sleep w/ muscle ridgity, this pain will go away after movement of body and urination, extreme fatigue, body aches, decreased appetite, itching, depression and some anxiety. CBC, and u/a are normal , Abd ct shows only kidney stones. I feel better on the cipro but once it is stopped my symptoms continue. I know that something is wrong, either with my kidneys or possibly and adrenal gland issue... My main complain is the waking in severe pain with inability to move. I am scheduled to see an internist soon but I was hoping you could maybe shed some light on what may be going on or possible diagnoses I could have him check for.