Hi Limpopo,
we just finished that trip, Cape Town-Cairo and are busy with the absolutely unnerving customs in Egypt.
Here's the route we took:
CT-Windhuk-Grootfontein(Maori Camp is great)-Caprivi Strip-Vic Falls-Lusaka-Lilongwe-Nkatha Bay-Tanzania-Iringa-Singida-Arusha-Nairobi-Isiolo-Marsabet-Moyale-Addis-Kombolcha-Lalibela-Gonder-Gedaref (don't stay there, if you don't have to)-Khartoum-Kabushiya-Karima-Abri (stay at Nubian guesthouse)-Wadi halfa (Cangan Hotel is quite good)-Aswan-Quena (not recommendable)-Safaga-Sokhna-Cairo (Isis Garden camp is nice)

Some basics: The route took us just over 2 months (covered about 400km per driving day, took some days for relaxing and visa-stuff), exept of the 180km stretch between Marsabet and Moyale and some parts in Tanzania it was all tarred. The Moyale road is getting better by the day.
Fuel problems you will get in Ethiopia and Sudan as a lot of gas stations don't have benzin or are closed and may be in Egypt, where some gas stations only sell 80 Octane. So make sure, that you fill up in the bigger cities and take an extra jerry can (10l did the job for us) with you.
Spare tires: Best is, if you take some with you, in Nairobi (jungle junction) you might get some, but they might be those cheapos, which don't last long. Best is, if you put on Heidenau Scouts, they last the longest and are good on all terrains. Make sure, you got a puncture fixing kit and the required tools with you.
If you wanna go with on of those GS with the tall, narrow shocks, make sure you exchange that and the bearings beforehand for a more solid ones. In any way, take a spare rear shock with you.
Ethiopian Visa: Get it in SA, as you don't get it in Nairobi
Sudan Visa: Takes about 3 days in Nairobi, may be you can get it in SA.
Egyptian customs are as bad as you heard. We are currently in the process of getting the bikes shipped back to Germany, hopefully we will finish it today, which means it took us about 2 weeks. To avoid the heavy Egyptian customs I suggest, you take a ferry to Jordan or Saudi Arabia and ship from there, prearrange it, if you wanna be fast.
Another way to avoid it is going via Libya to Tunis and ship it from there. Libya is supposed to be amazing, we really regret having the shipping prearranged and thus not being able to go there. Visa can be arranged in Cairo, find out about the countries situation with travellers you meet on the way, coming from there.
Israel is a possibility too, but at the moment it is not advised to go in the northern Sinai. And at the Israeli border and at customs you have to unpack your whole bike and scan all you belongings (took some guys 8hrs and more).
Hope, those infos are of use for you, good luck with your trip.

Mulle