so I have my ticket in hand for Mali and Burkina Faso leaving end of this month..

In Mali, I plan to take the pinasse from Mopti to Timbuktu and spend a week or so in Dogon Country.
and then 2 weeks in Burkina..

Do I need to make travel arrangements now? Does anyone have recommendations for a local guide who is cheap (no luxury traveling)

any other advice for a single female traveling alone to west africa for the first time?

Hi,
I've actually never been to BF or Mali (you're lucky they both sound amazing), but I've spent several monthsin West Africa (Ghana, Togo & Benin).
I have many friends that have been to Burkina, but don't know anyone who's been to Mali unfortunately. Anyway, BF sounds pretty similar to Benin. As in, making arrangements before you go is definitely not essential, and probably pretty tricky. Just go with the flow, use public transport and have fun. A guidebook would be helpful in finding out cool things to see, places to go and Hotel names (or if a certain place even has a Hotel!)
Do you speak French? This will definitely influence your experience, especially with local interaction.
As for Mali, it seems a little more touristy and tour companies are probably more available and easier to organize. I'll let somebody else cover this topic though!
Good luck and have fun! West Africa is an amazing place. I'm hoping to go to Burkina Faso from Benin next summer.