What is the primary source evidence for the theory that the African Ancient Egyptians are not black Africans whose origin is sub-Saharan Africa?

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The origins of the Ancient Egyptians remains very much an open question. The latest DNA study that I'm aware of suggests that Ancient Egyptian populations may have more common ancestry with populations in the Near East and Europe than with those in Sub-Saharan Africa. That said, the available evidence is limited and future research may change our understanding.

I'm not sure that US definitions of 'race' have any application to a discussion of the origins of the peoples of Ancient Egypt, so I do not propose to address them here.

I should, perhaps, address some of the other points you raised in your question though. I'll begin with the claims by Yosef ben-Jochannan that you quoted in the question here, and in your (now deleted) answer to the previous question that you mentioned.

Firstly, as can be seen clearly in this image, the papyrus of Hunefer is written in hieroglyphs, not hieratic, as he claimed:

Papyrus of Hunefer

Secondly, I have transliterated and translated that document myself, and the passage he 'quotes' does not appear anywhere in the text.

Thirdly, the supposed quote also does not appear anywhere in Budge's translation of the Ancient Egyptian Book of the Dead or his translation of The Papyrus of Hunefer.

A charitable view might be that Yosef ben-Jochannan was simply mistaken in his reading. A less-charitable view might be that he simply fabricated the quote to support his argument. In either case, I think it can be safely discarded for the purposes of the questions here.

In the case of the ancestry of Ramesses III, it is worth going directly to the DNA Tribesยฎ Digest February 1, 2013. Their conclusion states:

These results indicate that both Ramesses III and Unknown Man E (possibly his son Pentawer) shared an ancestral component with present day populations of Sub-Saharan Africa. This preliminary analysis based on eight STR markers does not identify the percentages of Sub-Saharan African ancestry for these ancient individuals. This preliminary analysis also does not exclude additional ancestral components (such as Near Eastern or Mediterranean related components) for these ancient pharaonic Egyptians.

In addition, these DNA match results in present day world regions might in part express population changes in Africa after the time of Ramesses III. In particular, DNA matches in present day populations of Southern Africa and the African Great Lakes might to some degree reflect genetic links with ancient populations (formerly living closer to New Kingdom Egypt) that have expanded southwards in the Nilotic and Bantu migrations of the past 3,000 years.

In this context, it is also worth mentioning that the haplogroup E-M2 (formerly referred to as E1b1a) is believed, on present evidence, to have originated in the Horn of Africa around 42,000 years BP. Frankly, given the proximity to the Nile Valley, it would be surprising indeed if this haplogroup were not represented in Ancient Egyptian populations.

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