South Africa is your best option if you are looking for a less-hassle procedure. Its the most developed country in the continent.
Walbis Bay in Namibia is a quite busy port as well. Lagos in Nigeria, Dar es Salam in Tanzania, Dakar in Senegal & Tema in Ghana are also very busy ports.
You can check the WWL RORO lines connections from South America to Africa. They have a very comprehensive online service.
I would also drop an email to these guys: African Overlanders. Their business is located near Cape Town area for some advice & insight. Maybe they have some connections in Namibia (which is also quite organised for African terms).
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