Interesting, you are talking about pre dynastic period, before the formation of the nation state? Correct. They may have influence (what is NOW South Sudan) which i doubt, but were depicted in the ancient art, that is a resounding yes. The bottom line question are they pharaonic people, questionable. For my perspective reading about their culture besides cattle culture, which many cultures practice around the world anyway leave doubts to such analysis.
No, READ my sources again, they specifically state Egypt. I don't know why you think Egypt(especially during the wet Sahara phase) was some type of barrier and cut off from the rest of Africa. Nowhere do they state "South Sudan", come on...
As for cattle, has it said that many cultures around the world share the same cattle culture similarities to the Ancient Egyptians like Nilotic people of the Sudan do? No. Anthropologists have long noted Nilotic people of the Sudan to having cattle culture more similar to the Ancients. The sources are right in front of you. Also Nilotics today are semi-agricultural pastoralist just like the Ancient Egyptians during the predynastic period were.
Not only that, but the STR values by DNAtribes(which was posted mant times in this thread) which was originally acquired by Zahi Hawass show most of the 18th dynasty Amarna mummies to cluster more with Nilotic groups.
I mean why the heck would any of this be suprising? Like I said Nilotic speakers lived on the Nile Valley longer than anyone else, but we know this...
"Accordingly, through limited on number of aDNA samples, there is enough data to suggest and to tally with the historical evidence of the dominance by Nilotic elements during the early state formation in the Nile Valley, and as the states thrived there was a dominance by other elements particularly Nuba/Nubians. In Y-chromosome terms this mean in simplest terms introgression of the YAP insertion (haplogroups E and D), and Eurasian Haplogroups which are defined by F-M89 against a background of haplogroup A-M13."---Hassan 2009
Now which state in the Nile Valley is he referring to?
Also the "ancient gods" South Sudanese, and many African groups worshiped was a contrast in what was practiced in the ancient Nile Valley, and from what i read South Sudanese did not worship Isis
Kawa temple North Sudan
http://www.saylor.org/site/wp-content/uploads/2012/01/1.8-AEGISOFISIS.pdf
Other African religions
Nuer Religion
Dinka religion - Wikipedia, the free encyclopedia
Yoruba religion - Wikipedia, the free encyclopedia
Odinani - Wikipedia, the free encyclopedia
I hope you know that ISIS is said to have southern origins. And again you are looking at the Nile Valley in a bubble. And ISIS was just one god, but anyway just because Southern Sudanese did not worship ISIS(though she was said to come from more southernly parts) doesn't dismiss that Ancient Egyptian religion and other African religions don't share a same origin from the wet Sahara or that there was no influence.
And what about this?
"It is doubtful whether Osiris can be regarded as equal to Tammuz or Adonis, or whether Hathor is related to the "Great Mother." There are closer relations with northeast African religions. The numerous animal cults (especially bovine cults and panther gods) and details of ritual dresses (animal tails, masks, grass aprons, etc) probably are of African origin. The kinship in particular shows some African elements, such as the king as the head ritualist (i.e., medicine man), the limitations and renewal of the reign (jubilees, regicide), and the position of the king's mother (a matriarchal element). Some of them can be found among the Ethiopians in Napata and Meroe, others among the Prenilotic tribes (Shilluk)."
(Encyclopedia Britannica 1984 ed. Macropedia Article, Vol 6: "Egyptian Religion" , pg 506-508)
Who are the Shilluk people and where do they live today?
Anyways to back up my point with the wet Sahara and their influence on Egypt...
Art of the Egyptian Nile flourished much later than that of Saharan and Sudan Africa. The Sahara representations of oxen with discs between their horns is much earlier than those of the cow-goddess Hathor. The hawk delicately carved on the sandstone plaque of Hammada el Guir is much earlier than the ram of Amon [known from the 12th Dynasty onwards]. When Andre Malraux looked at the animal heads at Oued Djera, he considered them to be "forerunners of the Egyptian animal deities." The same no doubt holds for the bird-headed goddess at Jabbaran. Semi-naturalism only appears in Egypt in the Gerzean period and is derived from Saharan ox period carvings ... Egypt had a tremendous influence on the interior of Africa ... but what is even more certain is that the prehistoric civilizations of the Sahara is earlier in time ... It was only from the so-called "historic" period onwards that Egyptian civilization achieved that splendor as a result of which everything is now attributed. But where art and technology is concerned, the focal points were originally in the modern republic of the Sudan, in East Africa, and the Near East. Moreover, the prehistoric Sudan owed much more to southeastern influence that to those from the Near East (1981:676).
Continuing...
Thus, the ancient Egyptian belief that divinity can be manifested in any form has strong pan-Africanist roots. Among cattle-owning societies in Africa, cattle are symbols of wealth and serve to define as well as distinguish status. Old Kingdom tombs depict cattle as large parts of a noble's holdings. Cattle provided the means for forging new relations of cooperation and interdependence. Cattle were valued for milk and cheese, but were occasionally slaughtered for religious offerings (Beidelman 1960; Bloch 1971; Rigby 1969). In common with other African pastoralists, the Egyptians practiced horn deformation on special cattle. Egyptians worshipped cattle as beneficent deities. Deities with bovine aspects echoed the importance of cattle in Egyptian society. Apis, the bull deity of Memphis, was a national deity. A bull with special markings and color was sought and, once located, was enshrined at Memphis with great honor. When the Apis died, he was embalmed with solemn ceremony and buried in the vast catacombs at Saqqara, called the Serapaeum. It should be noted that some ox masks of the Bidjogo peoples of West Africa and Apis bulls have a triangular forehead design. Besides Hathor and Isis, Neith and a lesser-known deity, Bat, occasionally were depicted in bovine form. Cow deities provided milk and nourishment for the pharaoh.
Egyptian myths and stories feature cattle. In the Story of the Two Brothers (Lichtheim 1976:203-210), a pair of brothers are grazing animals, and one brother takes on the appearance of a bull. Cattle formed an important part of the booty in Egyptian and other African military raids on neighboring peoples. The Maasai, for example, believe that God gave them all the cattle in the world. They thus feel that they have strong kinship ties with cattle (Rigby 1992). This culture is well myth of many African societies, in the archaeological record, and in modern African religious and cultural practices. Animal deities and animals, then and now, continue to play a central role in everyday spiritual, cultural, and economic life of African people.
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Now YOU tell me in which African culture is cattle so religiously worshiped and seen as being economically wealthy by having a lot of them? I mean is this not a coincidence?
Again which African culture places such high values on cattle? Hmmmm....
But anyways the fact is that Ancient Egyptian religious traits can be found throughout Africa and this is because of a common origin in the wet Sahara and those African cultures influencing Egypt culturally.
By reading this and do a honest comparison, it contrast what was practiced in the nile valley. In all honesty, when Afrocentrist make claims that the population today in North Sudan and Egypt are not descended of the ancient culture it becomes problematic, and a war of words pursue, and i understand that most of this does not have to do with us, and it mainly the social issues in America.
That's only if you look at Nile Valley civilizations in a bubble and not as continuous African culture of the Sahara and Upper Nile Valley. This type of thinking is why Egyptologist sometimes think the Ancient Egyptians were aliens, instead of looking at their African base.
As for the rest of your point, I know I am not denying modern Egyptians and Northern Sudanese are not descendents of the Ancient. But lets not ignore the fact that modern Egyptians especially have extreme foreign admixture(especially those from northern Egypt) and many studies back this up. But fact is the Egyptians and Nubians were NEVER a homogeneous people, like you seem to look at them. There were many type of "Nubians" that are considered more related to modern Beja people and nomadic people(who most Sudanese descend from), while others more related to Nilotics.
And I don't get what social issues in America has to do with this?
aint been black for real since 1600bc up north 
