It’s not such huge deal really. In late 2016 I arranged a flight down to Mozambique from the UK at short notice (in 14 days). Mike Gray at White Rose arranged the avgas, handling and overflight/landing permits with his usual friendly efficiency. The routing was:
LGIR Heraklion
HESN Aswan – bowser, pay in USD, meter overcharged me but it was night and I was surrounded by solders…spectacular destination though (Old Cataract Hotel)
HSSS – Khartoum, drums, bring our own pump, USD
HKLK – Lokichogio – drums trucked in from Nairobi and pre-paid. Kenya CAA very helpful, pre-paid landing fees for Nairobi.
HKNW – Nairobi Wilson, bowser, USD
FQPB Pemba – BP card
FQMA Maputo – BP card
The East Africa route is easier as GA is prevalent and avgas widely available – phone ahead of course. It gets more problematic north of Kenya which is where you need the overflight agent to sort things out with known and trusted handling agents. Especially if you are flying a twin, take several thousand USD stashed away somewhere safe. Make sure you have lots of multiple copies of your Gen Dec. The power of the rubber stamp. The handling agents will keep you right.
We have recently been to Botswana (Maun) and Harare (Charles Prince), avgas by credit card, welcoming and easy. Same all over SA and Namibia of course.
As you probably know, the GA scene in South Africa is very healthy – we have been to 4 fly-in / airshows in the last 6 weeks in Pretoria / Lowveld / KZN / Swazi. Lots of classic aircraft and world class aerobatic teams. You might want to check out what’s on before you depart. There is an air rally event in Botswana in June which looks interesting: Race for Rhinos www.airrace.co.bw
NeilC, did you have issues organising insurance for North Sudan?
Yes, that was a challenge, but it was the only re-fuelling option. I did not stay long and thought of General Gordon 
. https://en.wikipedia.org/wiki/Siege_of_Khartoum
The rest of the trip was OK. I suspect all ferry trips have the same issue.
Nice plan!
We flew to Dakar two years ago, basically halfway down the western route. Avgas was no problem. We needed permits in Marocco and Mauretania.
See http://www.abeam.be/back-to-africa-full-8-day-trip-report/
Enjoy
@vrh here has done multiple trips part way down the west coast, from France. It is a popular route for a group of French pilots, possibly partly because those countries are French speaking. However lots of GA has gone down to Morocco. Thre is some debate whether permits are required, for Morocco and beyond…
We needed permits for south-Marroco (western sahara)
You should contact www.prepare2go.com they have quite a lot of experience with sep flying in Africa
They do fairly expensive organised group events; occassionally “advertised” here
If I was doing this I would contact the overflight agents in post #5. Ultimately just about everybody uses one of these on these routes. They have the contacts in the national CAAs and know who to “lubricate”.
A long range plane makes it all much easier (I believe the current UK-Joburg record is held by a specially fuel-tank-modded plane with a 2500nm range which had to make only one stop, in the middle of Africa) but you still need overflight permits.
On the east route, many have commented that if you have the range to cross all of Sudan, from Aswan in Egypt all the way to Kenya, that takes out the worst bit. Many stories of having to bribe pay soldiers to sleep next to the avgas drums in Sudan to make sure nobody steals them during the night
I am not sure where Peter has his information from but Khartoum is one of the friendlier places to stop over on the eastern route. I have used it on three occasions in the last four years and with each, the avgas barrel was there on arrival, refuelling (take your own pump) was quick and we were well looked after by friendly handling agents with a good hotel nearby and efficient transport to and from.
The need for ‘douceurs’ begins south of there.
From pilots who flew there, though apparently not in the last 4 years. Thanks for the up to date feedback, JulietBravo.
