It sounds like a great idea, but a very difficult one. First you have to consider the amount of water and fuel that you have to carry. You may get water from local wells and local villages, but petrol will be quite difficult to find and expensive (north Chad) when you do so.
I think you have forgotten that between Niger and Sudan there is yet another difficult country to travel on, Chad.
The riding will be quite demanding at best of times, specially north of lake Chad and from Chad into Sudan. It will be extremely hard two up, let alone carring the water and lots of fuel that you'll be needing. The solution will be to team up with a 4x4 or a overland truck (I meet one doing that route!!!), so at least they can carry your extra weight, otherways you'll be relaying (and paying for) local traffic.
As far as I know all the border still open, and with the right preparation and support is a great route to do. If you decide to go ahead and need more info, let me know.