My experience is that it's surprisingly difficult to get accurate information once you are on the road; you may find things are "interdit" without ever finding out the real reason!
For maps for Mali and Niger, the IGN 1:200000 are ok - available online at ign.fr.
Realistically your route is going to be quite restricted on the Sahara section. Assuming you have a vehicle, your (compulsory) guide in Algeria can be trusted to pick a good route depending on what's currently open, and what time you can afford.
I used Voyages Tanezroufte and found them very flexible - final route agreed the night before departure, but the security situation has deteriorated since t hen (2007).
In Niger, you're basically going to be heading directly for Tahoua I imagine.