I'm also a solo female traveler. Between that and my fairly minimal French, I didn't feel comfortable doing it independently. After getting some recommendations and contacting a few companies, I had Toguna Adventures (which is run by an American woman married to a Malian man) make my arrangements.

I had also looked at various small group tours, but having something customized made it easier to tag on Burkina Faso. The most amusing part of the arrangements was my phone conversation with AS (whose miles I used on AF for the plane tickets.) After I told the guy I wanted to fly from IAD to Bamako, Mali and back from Ouagadougou, Burkina Faso, he asked me, "are those both in France?"