Is there a common thread that unites early African cultures?
There is no universally accepted answer to your question.
Some scholars believe that each region in ancient Africa exhibited unique cultural mores. They believe that even within the same region (e.g. West Africa), cultures may have varied widely from group to group.
Harvard University professor Henry Louis Gates Jr. is a champion of this school of thought. He argues, for example, that the Nigerian Igbo culture was an egalitarian culture in which gender roles were non-existent. The Ashanti in the other hand, were patriarchal with a strict gendered division of labor (According to Gates).
Other scholars believe that there exists a strong common thread between different communities within the same region, and possibly between all cultural groups in Africa.
Molefi Asante is a champion of this school of thought. Asante, head of the Temple University Black Studies Department, argues that all African cultures exhibit the same cultural traits and share similar spiritual and cosmological beliefs.