Update: Ah, I take you're going to cross north to south, meaning you only have a (comparatively) tiny slice to go through. Then you'll likely survive, good luck getting the Angolan visa though...
From what I remember, the southeast corner, bordering Uganda and Rwanda, is/was the most unstable. Burundi had issues because of the election. Not sure where it stands now. I did not go to Burundi since the travel visa was expensive. I was traveling on public buses, so even a three day visa might not be enough.
Thanks for the info. It seems virtually every country on the continent has issues around elections, and should be avoided. DRC, Gabon, Ivory Coast, Mali, etc. all have recently been not-good places to be due to elections
Enjoy your time. I dream about going back to Africa. If I had to do it again, I would do it exactly like you are doing, using self-transport. Besides setting your own schedule, you get to pack your own food. Much of Africa simply does not have stores. However, I would travel with others.
My research says Burundi is pretty stable.. I was planning to go there. Do you recommend otherwise?