If you were my patient, I would recommend that you go through with the colonoscopy.
Your doctor is correct that your symptoms aren't consistent with endometriosis. Your story sounds more consistent with IBD, but I am hoping that your MD would only find IBS. Another diagnosis to consider is Fibromyalgia/ chronic fatigue.
This is now a fairly well recognized syndrome and there are some therapies that might help.
Watch out for weight gain if you are on depot provera--that stuff is terrible! In fact, it could be causing some of your symptoms too!
(continued) I saw my Gyno again last week and she is hesitant to give me a laparoscopy because she is not sure that Is endo. She strongIy feels that if it was endo the Depo Provera shot should have cleared it up. I asked her about my muscle cramps, joint pain, ear pain and low grade fevers. She said that they are not symptoms of endo and it could be an autoimmune disease but I read on several endo sites that they can be associated with endo. She sent me back to my regular physician to test for autoimmune diseases. They tested for Lupus, Rheumatoid arthritis, and thyroid disease along with X rays of my joints. They all came back negative, but showed arthritis in my right hand. So, then I visited a Gastroenterologist, he didn't think that my pain was GI related, but suggested a Colonoscopy to rule out endo in the bowels and GI diseases. He also, prescribed me Hyocsamine. It seems to help with the abdominal cramping. I also started the endo diet because I am having food triggers, I noticed that my pain is stronger after having coffee/caffeine, chocolate, dairy products and alcohol. I don't know where to go from here. I am very frustrated. My Gynecologist is offering me a laparoscopy, but does not have any openings till April or she suggests trying the Lupron shot (which I do not want to do because of the side effects). My regular physician wants to take an MRI of my heart and CT scan of my brain to figure out what is triggering the muscle aches and joint pain, and the GI specialist is suggesting a Colonoscopy. Since my lap is not scheduled till April, I am considering the colonoscopy, but I am so confused and I am not sure if it is Gynecological or Gastro related. Also it has been very difficult for me to concentrate lately. I am stuck in a 'brain fog' any advice or feedback you can give me would be very helpful.