Cliff: That covers all of Africa I have been to. It doesn't change too much.
Grizz: If there is a major UN mission in the country, Plan on it not being secure. Heck, a lot of Africa is not too secure even without UN troops. And the UN Missions are usually not too much help to outsiders. The contractors that fly for them usually are.
Slip: I have fuel cards in the aircraft but except for Lusaka, J'berg and Cape Town, I haven't been able to use them. The airports and fuelers will take local currency or hard currency. They prefer hard currency as they can make a little extra money at your expense. However, some areas go over board, Like Rep of Congo.
Reaper: I would plan on using a handler. At least until you get to know the area better. Some places you will always need a handler, other you will not. However, when you get there you can find a local handler to handle you when you need it. I am based here and fly into these places on a very regular basis and I still need a handler in some places.
Another word to the wise. Stay at 4 or 5 star hotels only, preferably 5 star. And get your reservations early. Good hotel rooms are hard to find at times. And always take your reservation numbers with you.
Filing the flight plan is not the problem. That is usually quite easy. It's the overflight and landing permits that can be the issue. 24 hours minimum and usually 48 hours in advance. Monday through Friday, or Sunday through Thursday for the Muslim countries.