Jeddah as a connecting point
Definitely, Jeddah is not a good connecting point between Cairo (CAI) and Johannesburg (JNB). Moreover, in case of using multiple tickets for connecting flights, there will be a risk of potential problems in case of late arrival of the delivering carrier.
Simply, two separate tickets mean two carriage contracts. On the other hand, the participating carriers shown on ONE ticket covering all flights from the origin (CAI) to the destination (JNB) will be responsible for any possible delay, mis-connection, or layover.
What about flying with Kenya Airways through Nairobi, or with Ethiopian through Addis Ababa?