Just to clarify, I'm not referring to Africa south of the Sahara. I hear numerous accounts about written scripts found in Sub-Saharan Africa. From the Mali Empire, Songhai, and Hausa kingdoms and all of the Swahili states that minted their own coins bearing Arabic scripts. And of course the Ethiopians who still use their own indigenous script to this day. I'm already well aware that there were plenty of literate states in S.S Africa. However any and every time there are any references to the history of Africa (including the previously mentioned states) it seems to always reference North African, Arabic, or European sources. Were the S.S. nations simply not using their script for recording history? Was it used specifically for math, science, and religion? Timbuktu has over 700,000 manuscripts dating from the 1200s yet all references I see about the empire come from Egypt, Morocco, and griots. Why not refer to the 700,000 scripts in Mali? The Swahili coast were very advanced with stone buildings, sewage systems, sail ships and used Arabic writing systems. Where are all of their books? Were they not used for recording history? Yet again... where are the written accounts of these places? The Gedi Ruins are lost to history due to lack of written records. Why?
Read the section titled "Internal Sources" in chapter 8 ("Arabic Sources for African History", by John Hunwick) of the book Writing African History (2006). It contains some information about relevant internal sources for areas south of the Sahara (besides those in Ge'ez).
But the best answer to your question is that most of the relevant sources were either lost or destroyed (during invasions). We have clear contemporary written evidence from outside observers for the existence of numerous scholars in Ghana, Kanem, and Mali, and we have evidence that some of their scholars who went to North Africa were held in high esteem there because of their piety and learning, yet none of the relevant works (whether of a historical nature or not) from these scholars survive. For example, shortly after his pilgrimage, some of Mansa Musa's scribes composed a book and sent it to the sultan of Egypt, but that book is now lost.
Even when talking about later (later than the time of Ghana or Mali) written internal sources, probably not that much has survived. For example, the historical work written by Masfarma Umar ibn Uthman, describing the exploits of the Bornu sultan Idris Katakamarbe is lost. And a 16th or 17th century book by a certain Baba Goro called Pearls of Beauties Concerning What is Related About Some Kings of the Sudan (or alternatively, The most beautiful pearls from the history of certain kings of the Sudan) is also lost.
(I realize that the poster is banned now, but I provided an answer just in case he ever checks on his thread at some later time.)