I've got no waypoints for you, but can give you a rough idea of the route I did in 2006. Get your map out and find these places:
Egypt to Sudan and Ethiopia - cross Lake Nasser from Aswan to Wadi Halfa, then follow the Nile to Khartoum. Head west from there on the main arterial to Ethiopia, crossing at Qallabat to Metema in Ethiopia.
Ethiopia to Kenya - cross at Moyale. At the time we crossed, it was bandit country, so we had to join an army-run convoy through northern Kenya
Kenya to Uganda - cross at Tororo. The road to the border from Nakuru was reportedly bad, so we were advised to get off that road and get to Kisumu via Njoro, Molo and Londiani, so we crossed the border at Busia. You'll have to find out more about the state of these roads, but Kenya certainly had some of the worst roads on offer on our entire trans-African trip.
Uganda to Tanzania - cross at Mutukula. Once again, bad roads in this part of TZN, so we took the ferry from Bukoba to Mwanza. Not sure it was the right decision as the ferry was scarey for the car. It had to be crane-lifted onto the boat and the crane was only rated to 3 ton because parts for maintenance were not so easily available! We survived the banana boat.
TZN to Malawi - cross at Kyela on the road south of Mbeya through Tukuyu.
Malawi to Zambia - cross at Mchinji and on to Chipata in southern Zam.
Zambia to Namibia - cross at Sesheke/Katima Mulilo
And finally, Nam through Bots to SA - we took the Trans-Kalahari highway, crossing into Bots at Buitepos and thence into SA at Skilpadshek.
It's basic, but maybe this will help. Nothing you wouldn't find in any of the guide books. If you can find Bradt guide books, they are the best for Sub-Saharan Africa. Rough Guide was best for Egypt.