In regards to hotspots, there's not many alternatives. Nairobi would have to be top of list. You can get some parts, some tires (costly though) and access to a good mechanic through either Jungle Junction (where most overlanders stay) or through the KTM dealer. After that, the availability of parts and big bike mechanical advice decreases significantly.
Having said that, in general, availability and prices of parts won't be as good anywhere in Africa as it is in South Africa. Other than oil, I would plan to be self sufficient once you leave SA. For tires, I would either start on a new set I knew would make it (eg. K60) or carry a spare rear, ship a set ahead, or try to contact JJ or the KTM dealer to see if they have my size and I was ok with the price. In summary, on the east coast it's sort of ride from SA, pit stop in Nairobi, and then plan to make it all the way up to Turkey.