We just did West Africa Route to Cape Town in 110 Defender - see Latest news / About us - Langebaan Sunset - Stonehenge UK to Cape Town SA - 2010/11
We have posted a stack of info: gps, way points, budget, etc..etc...happy to take any questions offline.
Regards Carnet - Egypt is 800%. West Africa Route uses 150% as the max so its cheaper for the Carnet security to avoid Egypt. Our Land Rover was 14 years old and had a second hand value of £3000. So our security for Carnet was £3000 x 1.5. we used Bank Gurantee from First Direct - simple, easy and they do it with minimal fuss. RAC Paul Gowan liasie with First Direct all the time - its a good service.
I would get the Carnet - depositing money at borders in West and Central Africa and hoping to get it back is NOT advisable (read our post about the Rosso crossing into Senegal). The Carnet is worthwhile getting as it is VERY useful when you get stopped at checkpoints (esp. Senegal, Nigeria).
I would suggest you go West Africa if you have time and want to go on the road less tarveled. There is less commercial overland traffic, North, West & Central Africa is amazing and people are great. Its also cheaper than East Africa. Southern Africa (Nam, Bots, SA) is expensive but there is also a lot to see. Read our site to get a feel for it.
If your pushed for time East Route will be quicker and still fun but you have to work out the Egypt deal..... Just avoid the big campsites frequented by the "tour bus" package deals that like to arrive late, party, and wake up at 5am to depart at 6am.... they are sadly spoiling it for everyone but that's mass tourism for you ;-)