If you are using jet fuel then availablility shouldn't be a problem. If you are unpressurised then take plenty of oxygen....especially if you are going to Addis; those mountains are fierce. Don't do them first time in the dark.
I think that your schedule is somewhat optimistic....and I plan these things for a living. Two legs in a day is about what you'd expect. There is a lot of messing about on the ground - even when you are paying a handling agent.
Arriving at Wilson after about 5pm will mean that you have nowhere to park.
Lilongwe is an easy, and cheap, stop between Nairobi and Joburg.