We will be heading the other way, riding every day. South Africa, Botswana, Zambia, Tanzania, Kenya (end of first leg), Ethiopia, Sudan, Egypt (end of second leg).
The roads from South Africa to the middle of Kenya are all paved (Africa pavement, pot holed and nasty). As far as I know, from there on, the roads are pretty much untarred until Egypt, with tall mountains and mud during the summer in Ethiopia.
I believe this route is the quickest route through Africa, with the best roads and the most civilized countries. Still, don't expect to get through qucikly. We expect to spend 20 days of riding to get from Cape Town to Nairobi, a distance of about 6.000 km, an average of 300 km a day (and that is the easy part of the route). From there on, it is about another 6.000 km which I expect should take much longer, maybe an average of 200 km a day. In Africa this translates into long days. I have never done this trip before, but I doubt that anything more than 400 km a day is realistic. On our first leg Cape Town - Nairobi, we will ride anything from 2h15m a day to 8h40m, with most days translating into 5-6 hours of riding.
These are of course only my personal rough estimates, the real deal may end up being far slower or faster. Never the less, I've come to understand that by most standards, doing this distance in 20 days is considered fast. I'd even consider crossing Africa in two months to be fast, even if you rode every day much of the day! Then again, I believe the dakar rally this year was 9000 km in 14 days...
Don't forget that you will likely experience several punctures, hassles with officials of all sorts, changing money, doing repairs and maintnance, border crossings, etc. The red tape in Egypt is supposedly a pain in the a**!
I have myself tried to get ahold of this information from others, but it seems as though most people take their time getting through, not rushing it like you and me.
Don't take my word for it though, I may very well be wrong in much I say here. You should check out more sources before you make up your mind.