There are alot of possible routes from SA to Egypt. At the end of the year I'll do the same trip but from north to south. I decided to go along the east. So in your case: SA, Namibia, Zambia, Malawi, Tanzania, Ethiopia, Kenya, Sudan, Egypt. It all depends on what you want to do, see and how much time you have. East means a majority of tarmac roads, west means more dirt tracks.