Pelvic pain, low progesterone levels, ovarian cysts, what is wrong with me?

Hard to say. These may not be related to each other. Many things can cause pelvic pain, if you have large ovarian cysts (>4cm) they may be the cause, but smaller ones less likely to cause pain. Low prog levels (&small ov cysts) are both normal during certain phases of menstrual cycle. But low prog can cause mood sx, anxiety, sleep disturbances. If you have these natural Progesterone tx may help.