I have been around Africa a bit. If it is native African species you want then there are a few biomes you might want to visit.Kenyan/Tanzanian/ethopia, highish areas,
My experience of Ethiopia was that it is a beautiful country, with amazing culture and mouthwatering food - FAR better than any Ethiopian food I've ever tasted in the US - but not that it was great for rare fruits. The most produced crops are mango, banana, papaya, avocado, citrus, grape, and pineapple. I had guava there. The fruit was delicious, and they have favorable growing conditions for a lot of fruits. But, there is not really an incentive to grow much variety in that region since money is made off of crops like coffee, teff, etc. Anybody who has the ability to intentionally grow something, will tend to grow what supplements their income - not just their personal tastes. This is also reflected in what you can buy in the local markets. Also you have to keep in mind that the Eastern/Horn of Africa region is heavily affected by dry vs. rainy season. The winter will be dry season for them. So most areas will have desert conditions. I was there in the rainy season when the Blue Nile was overflowing and looked like Niagara Falls.
I would highly recommend it as a country to visit, but not for rare fruit unless you have a specific contact you know of who can hook you up. On the other hand, rare and unique culture (including exotic dishes), they have plenty of! I spent 3 weeks there, traveling all over the country, and made lifelong friends and had amazing experiences that changed my life. I long to go back soon.
If you wanted to give it a try, I would focus on the market in Addis Ababa - Addis Merkato - which is the largest market in Africa. If you can figure out how to navigate it (probably with a guide), you might be able to find the unusual fruits (and probably also vegetables) there. But it is HUGE, and what you find is going to be hit or miss. Like any market, time of day is also a big factor.
https://migrationology.com/addis-mercato-market/Consider time of year in your destination selection. The time you're going is going to limit you in a number of areas of the continent. You might need to focus on the rainiest areas for largest fruit selection.
I would agree that West and South might be better choices. Ghana and Senegal are easy to visit. Here are a few fruits you can find there:
http://www.itfnet.org/v1/2011/12/african-indigenous-fruits-with-potential-health-benefits/ West African crops also greatly influenced the Caribbean through the Atlantic Slave Trade. You can find fruits like ackee and miracle fruit there, as well as jaboticaba and june plum. They also grow katemfe fruit - Thaumatococcus daniellii - there. Palm fruits are a major industry in the region so you my also have some luck trying some you've never had.
Here's a list of some of the South African crops by month:
http://www.leadsa.co.za/articles/7258/seasonal-fruit-and-vegetables-in-south-africa and if you're interested it trying new-to-you varieties of more common fruits:
http://veggiebunch.co.za/fruit-growing-seasons-in-south-africa/The main problem is indeed the stigma of eating indigenous food, thanks to the scourge of colonialism. It's thus not profitable to grow or sell, so most of these amazing and life-giving crops are treated like weeds in favor of more industrialized and less nutritious plants. Finding the rare stuff involves serious hunting in remote regions, where local contacts and language/culture knowledge are going to be important, and where safety concerns can become more of an issue both because of wildlife, and because of a few uncool people who make life difficult for everyone. But the same could be said if you wanted to track down rare fruit in Alaska, or pretty much anywhere else... it's rare for a reason - because it's hard to get to and there's little money in making it easier for people. Remote areas pose the same risks all over the world for the most part. I will go into pretty remote areas, but there is a point at which I draw a line, particularly as a woman traveling. Jungle hunting is usually where that line has to be for me. But maybe as I get older that will be less the case, if people start viewing me as more of an elder, and less of a target.
There is a rare West African fruit I really want to try, but I can't for the life of me remember the name of it right now. It's a sour orange fruit that's really popular locally, and supposedly has a delicious flavor. I think it has health benefits too. But I forget where I found it, and where I wrote down the name! I do remember though that I was trying to find a source so I could grow it in my yard.