Hey Jude, (fighting the urge to include bad Beatles joke here)
General impressions of Windhoek having been there all of two times is that it seems to be a small capital in low population country which usually means limited supply and hence higher prices than a place such as South Africa.
A quick search should reveal prices and availability which probably then means that you could either buy in Cape Town and reverse the trip, or buy in a place like Jo'berg and do a loop to Windy and then down to Cape Town. All is possible, it's about 1,600 km from Cape Town to Windhoek so if you are willing to put in a couple of big distance days you could still easily fit your trip into three weeks.
As for the probability of finding something suitable in the price range you describe, that'll be a bit tougher and may place impossible restrictions on your trip. Or mean that you ride mopeds around Namibia which would be too bad as off the beaten path is what Namibia is all about.
You may want to consider looking more into renting, and if you doubled up you could probably find a good dual sport to haul you around.
Carnet is not needed, same trade zone. International drivers license seems to be required in a lot of countries in the world but usually providing a foreign license is enough to get you through.