Quichy is the undisputed king of African travel, but by the sounds Pat, you're going to give it a nudge for that title!
Sounds like a pretty challenging, but massively interesting trip.
To be honest, the one tip I'd give, is don't travel anywhere in Africa alone. Whether it be with another random traveler or friend or whatever. I wouldn't be going to places like DRC, Sudan (the southern part), CAR, Ethiopia, Chad, Niger, or Libya by myself.
I'm not as tough as Quichy when it comes to travel (also being hamstrung by a timid missus doesn't help either), so we did arranged tours for much of our travel in Morocco and Egypt. While travel in these coutries is generally fine, there are still places where an armed guard (a member of the military with an AK47

) will get on your bus to provide a secure escort. We did ours with a Turkish based company called Travel Talk and as far as organised tours go, these guys were nothing short of bloody awesome. Cheap, local guides, huge coverage of important sights and they also delved quite extensively into the average every day lives of locals. We met loads of locals in both Egypt and Morocco while on tour with these guys.
However, that doesn't solve your problem of getting from south to north.
Good luck anyway mate. Sounds like it's gonna be an amazing trip. All we ask is for regular write ups and loads of pics!