Has she had a colonoscopy? I would push for this. Black stool could be bleeding in her stomach or intestines or an infection. Is she seeing a GI doctor? She needs a specialist. Get her in a soon as you can.
Have her bring a list of ALL her symptoms (headache, etc), when they started (anything she can think of that may have been happening at the time to bring it on), and if anything makes her symptoms better or worse. Also, if she's ever had any issues with her digestion or anything (if she used to have an eating disorder, she needs to tell the doctor). Both of you sit down together and make a list of any questions you have to ask the doctor. You guys are paying the doctor, so he works for you. Don't let him give up.
Good luck. I really hope they find what's causing this soon.