I did Southern Africa in 2008.
You dont need a carnet for travelling on a South African registered bike. I travelled through South Africa, Lesotho, Swaziland and Mozambique. My friend did Tanzania, Zambia, Kenya, Namibia and Uganda with the same bike.
You do need a international driver's license, which is obtained from AAA. Simply bring 2 passport photos to any AAA office and they will issue it right there.
You dont need any special shots or Maleria tablets for travelling in South Africa itself, but as soon as you approach the borders (any border) its time to think about your shots.
I would not travel without insurance and you need a South African address to have liability insurance.
There are also several reputable rental companies that will rent you a KLR for $70-90/day with insurance etc. These bikes can be taken to Namibia and Botswana with an extra fee.
My experience is that if you are time limited (say 30-40 days or less), rent a bike. If time is no issue, then try to do a buy-sell deal. There is nothing more frustrating than sitting and waiting for paper work, when you could be travelling.
Also, you have to consider the currency exchange rates, so if you buy a bike: say a 2005 KLR for $4000 and pay in Rand. You have to pay to wire money to SA, then upon a resale, you have to pay to wire the money to the USA and if the currency has changed 10% agaist you, you coule be out $500 easily. It only gets worse if you get a more expensive bike (BMW or KTM Adventure.
There is also the issue with GPS. You'll probably want to purchase the Track4Africa maps and the Garmin Southern Africa Map and additional memory. Again renting is easier.
I cant tell you how much easier it is to simply fly in with your personal gear and some soft bags. Then get a ride to the rental company and you'll be in the most awesome country the next day!
Good luck and all the best
PS I'll be there in May-2010!!!!!!!!!!!!