re Is it possible to get a Carnet de passage and insurance for the bike in SA?

carnet yes - and I suggest that it's a good idea, although for Egypt it may be better to get one locally through an agent (arrange before arriving). FOr insurance most people buy the legal miunimum on arrival and this is easy (although a bit of a puzzle in Kazungula - see below).

re Are there going to be problems with border crossing

No - the Kazungula border is a bit chaotic, and in our experience the only one where it's worth enlisting help - simply to know where to go for the various steps in the process. The rest are straightforward (we have crossed all that you plan except Kenya/Ethiopia and further north.

...and importing the bike to Europe? What happens with the bike registration in SA?

To import the bike into Europe will depend on the local import rules for the country where you hope to import. Check with the local AA at both ends.

- Which Visas are problematic? Visas in Egypt, Ethiopia, Sudan must be obtained in advance if I am correct. Are fixers needed on this trip?

Depends on your passport. Our experience has been:

RSA - we needed visas ahead of time and were allowed to get them only in Caracas.

Botswana - we needed visas ahead of time and were allowed to get them only in Washington, USA.

Zambia - VOA no problem

Tanzania - VOA no problem

Rwanda - EATV online no problem

Uganda - EATV online no problem

Kenya - EATV online no problem

Egypt - VOA no problem, however we haven't entered Egypt from Sudan.

re What else do I need to think of?

Figure out what you want in terms of capturing your experience: for photos, anything from an iPhone to a DSLR with a couple of lenses. The key is how much weight/size you want to haul around. Sort out how to back up your photos (we upload to cloud storage as frequently as possible). A GoPro is a good option.

How to manage communication: smartphone with (relatively expensive) roaming capability or local SIMs (which you can but at borders), internet cafés.

Whether to take a laptop? Maybe - more space, weight, and worry (security), but a lot more capability in terms of photo storage, connecting for online bookings, permits, etc.).

How to manage money: combination of cash (USD are most useful) ATM cards, wire transfers (Western Union, whatever). We typically carry "emergency cash" and get money primarily from ATMs.

How to manage medical concerns: immunisations, emergency treatment, medications, etc. There is a heap of threads on various fora about malaria, yellow fever, dengue, etc., so read them and make up your own mind. First aid kit - you need one designed specifically for your needs - Is your blood type unusual?

Personal Travel Insurance: not only medical but also for activities which may not be covered by many policies.

Make up “In case of Emergency” cards with contact numbers, blood group etc.

Hope this helps.

PS: it'll be closer to 6 months than 4.