It sounds like your dr needs to give you an endoscopy, and not just a colonoscopy?
I was having severe stomach pains just before I started lyme treatment, and it got much worse during my first month of abx. I never had the dark black stools, but my dr told me that if it got that bad, or if I saw blood in my stool, to call right away. Neither happened, but because the meds she gave me were not working, she scheduled me for an endoscopy, and it turns out (as I suspected, even though she did not), I had/have an ulcer in my stomach. I also had a colonoscopy, and discovered other issues, but it was only the endoscopy (at least in my case) that revealed the ulcer.