Understanding the disparity of chronological sequence

"These people, whom we have called kings before, and shepherds too, and their descendants," as he [5] says, "held Egypt for five hundred and eleven years. Then," he says, "the kings of Thebes and the other parts of Egypt rose against the shepherds, and a long and terrible war was fought between them."
He says further, "By a king, named Alisphragmuthosis [6], the shepherds were subdued, and were driven out of the most parts of Egypt and shut up in a place named Avaris, measuring ten thousand acres." Manetho says, "The shepherds had built a wall surrounding this city, which was large and strong, in order to keep all their possessions and plunder in a place of strength.
Tethmosis [7], son of Alisphragmuthosis, attempted to take the city by force and by siege with four hundred and eighty thousand men surrounding it. But he despaired of taking the place by siege, and concluded a treaty with them, that they should leave Egypt, and go, without any harm coming to them, wherever they wished. After the conclusion of the treaty they left with their families and chattels, not fewer than two hundred and forty thousand people, and crossed the desert into Syria. Fearing the Assyrians, who dominated over Asia at that time, they built a city in the country which we now call Judea. It was large enough to contain this great number of men and was called Jerusalem.
 
Book 1, section 93

I shall quote Manetho again, and what he writes as to the order of the times in this case. He says "After this people or shepherds [8] had left Egypt to go to Jerusalem, Tethmosis [2], who drove them out, was king of Egypt and reigned for twenty five years and four months, and then died; ..."
 
Book 1, section 227

He [5] writes these words: "Those sent to work in the quarries lived miserably for a long while, and the king was asked to set apart the city Avaris, which the shepherds had left, for their habitation and protection; and he granted them their wish.
According to the ancient mythology, Avaris was Typho's [10] city. But when these men had entered it, and found it suitable for a revolt, they chose a ruler from among the priests of Heliopolis, whose name was Osarsiph [9]. They swore an oath that they would obey him in all things. The first laws he gave them were that they should not worship the Egyptian gods, nor should they abstain from any of the sacred animals that the Egyptians held in the highest esteem, but could kill them, and that they should not ally themselves to any but those that were of their conspiracy.
After making such laws as these, and others contrary to Egyptian customs, he ordered that the many the hands at their service to be employed in building walls around the city and prepare for a war with king Amenophis. He colluded with the other priests, and those that were polluted as well, and sent ambassadors to those shepherds expelled by Tethmosis to Jerusalem, informing them of his own affairs, and of the state of those others that had been treated so shamefully, and desired that they would come united to his assistance in this war against Egypt. He also promised their return to their ancient city and land of Avaris and plentiful support for their people; that he would protect them and fight for them if need be, and that the land would easily be subdued. The shepherds were delighted with his message, and assembled two hundred thousand men. Shortly they arrived at Avaris.
 
King Amenophis of Egypt, when he heard of their invasion, was perplexed remembering what Amenophis, the son of Papis, had foretold him. He gathered many Egyptians, and deliberated with their leaders, and sent for their sacred animals, above all those worshipped in the temples, and ordered the priests to hide the images of their gods with the utmost care. He also sent his son Sethos, who was also called Ramses, and only five years old, from his father Rhampses to a friend of his. He continued with three hundred thousand of the most warlike Egyptians against the enemy, who met them. But he did not join battle with them, afraid to be fighting against the gods. He turned back and returned to Memphis, where he took Apis and the other sacred animals which he had sent for, and continued to Kush, together with his whole army and masses of Egyptians.
The king of Ethiopia was under an obligation to him and received him, and took care of the masses that were with him, while the land supplied all that was necessary for the men's sustenance. He gave them cities and villages to live in, that was to be from its beginning during those fatally determined thirteen years. He sent his army to guard the borders of Egypt in order to protect King Amenophis. And this is what happened in Kush."
 
This is some of what the Egyptians tell about the Jews, I omit much for brevity's sake. Manetho continues: "Later Amenophis returned from Kush with a great army, his son Ahampses led another army, and both of them joined battle with the shepherds and the polluted people, and conquered them, and killed a great many of them, and pursued them to the borders of Syria." These and more accounts like them are written by Manetho.