If I read correctly you are asking:
Option One:
3-4 days in CPT
3 days Kruger
Then fly to SEZ via NBO
Option Two
3-4 days in CPT
Then fly to NBO
3 days Mara
Fly to SEZ
The distances are huge between CPT JNB then JNB NBO and JNB SEZ. I would stick to Kruger for the safari, so that when you fly thru NBO you are just in transit. Saves having to get a visa on arrival, swap to the local airport (Wilson), and hopefully have a connecting flight to the Mara, and then the vice-versa on the way back. More then likely you would have to O/N NBO at least once.
Stick to South Africa and Seychelles.