I've always thought about this, the Aztecs, Mayans, Incas etc. were even more isolated but they manage to develop astronomy, complex record keeping, pseudo writing and large urban dwellings and temples etc. whereas, Kingdoms in sub-Saharan Africa did not with a few exceptions like great Zimbabwe. why didn't knowledge of agriculture, animal husbandry and permanent cities flow down the Nile and into lower African kingdoms on the continent or by trade routes on the Swahili coast
Pending an answer from someone more knowledgeable than I am on the topic, "civilizations" did develop in central Africa -- this answer from u/commustar goes into the development of the Ghana/Mali/Songhai empires, and there's a lot more about "civilization" in Africa in this section of our FAQ.
Oddly, someone asked a question just like this in this thread, where I explain about the lack of monumental architecture and writing.
Otherwise, to answer these questions:
why didn't knowledge of agriculture, animal husbandry and permanent cities flow down the Nile and into lower African kingdoms on the continent
I'll simply say, there was knowledge of animal husbandry and farming, iron working, and large scale settlements in Central and southern Africa between 500 AD and 1000 AD onwards.