Hi Zenbiker,
great idea to plan this trip with your Partner. I did a lot of trips in Africa with my wife on the back, including Libya, Mauritania, Mali or Namibia and South Africa.
A lot of recommendations have been made, but what I would see first as the Basis: which route do you want to go and what Kind of tracks to you want to take.
Currently I´m on a trip on the western side of Africa - just back from Yaounde/Cameroun: we have seen fantastic landscapes enjoying tracks in the bush or the rainforest. But here I´m very happy to have a KTM 690 with just 15kg of luggage. Even so, I´m getting tired after our daily 200km trips. With my wife I made it with a KTM 950/990 ADV-S but less Kilometers per day!
Other Story is, if you stay on main roads and tracks on the East side of Africa...
Even though everybody should do it his way (People did it even with Vespas or Harleys), I found that the real difficult situations are not showing up on the tracks but on the way finding a nice campsite, a rivercrossing by canooes, the detour from a main road or the unexpected condition of a road that your map shows as tarmac (f.e. the main road in Senegal between Tambacounda and Kedougou has thousands of big potholes and a lot of big trucks Surfing around them - so most of the time you are riding on a 20 cm sandy Strip between bush and tarmac.
Reading that I think you know what my recommendation would be:
1. as light as possible. (At Speeds of no more that 80 km per hours power does not Count that much)
2. I always take knobbies (preferred type: Pirelli Scorpion Rallye). Even when you habe 95% tarmac and no Problems, it´s the 5% sandy track that Count - especially when you have the responsibilty for a Partner on the back.
3. you should know your bike very well. Even though you will find helpful mechanics everywhere, you should lead them. I personally check every screw by my self, because I have to rely on my bike in situations that are not comparable to Europe.
4. I never cared about tube tyres. You can repair them by yourself or find easily tyre repair - leaks are a common Problem for everybody...
So I hope you are not confused by all These opinions - I think you will find out and do it your way! Africa is fantastic!
best regards