From my own experience:
1. Safest, best way?
Easiest is along the west coast. Flying mid way thru the continent is a bigger challange. Sometimes no fuel for a looong time.
2. Permission into countries, is it a problem?
Use a handling agent for all the permissions. Doing it all on your own is a pain in the ass.
3. Fuel? JET-A1 of course. Long range tanks recommended?
Auxillary fuel tanks make sense.
4. Everything else!
Bring freshly printed USD and EUR in small bills. A generous tip makes things quick and easy.
It wont go as you have planned, so dont make your schedule too tight.
Take someone with you who did a similar trips in Africa.
PM me if you have specific questions.