Here is the translation of a letter from a French friend who crossed from Sudan to Egypt before riding back to Europe. Hope this helps...

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I did cross from Sudan to Egypt. The piste along the Nile river from Khartum to Wadi Halfa is beautiful and the Sudanese are lovely people. There is the ferry once a week from Wadi Halfa to Aswan, on Wednesday if I remember correctly. In Khartum, there is a Sudanese incredibly helpful and disinterested in money who runs a travel agency (Scorpion Tours). His name is Mahamat Tadrir and if you go to the Ministry of Tourism, they'll give you his address because he's very well known.

Entry in Egypt was hell for me because I did not have my Carnet. I had to leave my motorcycle in customs in Aswan, the time for my parents to ship me a Carnet by DHL. It is impossible to negociate, too many people are involved. You will see, these guys are nuts!!! You have to go through the customs (around 30 euros) then the traffic police rents you plates after you show them the papers from the insurance. With the guy from the customs who accompanied me during the entire formalities, avoiding the lines, it still took me 2 days. Nuts, I'm telling you. I hate this country for its paranoid customs legislation and its population rotten by mass tourism. After Sudan, it was really a chore. To leave the country, I took a ferry to Aquaba to avoid Israel. Jordanians are adorable and customs formalities are super simple. Then I crossed Syria and Turkey, where I tool a ferry to Italy.
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Pierre
http://photobiker.com

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Pierre Saslawsky
http://photobiker.com

I would have to agree with the fact that Egypt is a bearaucratic nightmare and that a lot of people have been negatively affected by tourism. But forutnately you will always come across one or two good people in each country which manages to even things out a bit.
As far as the Aswan ferry is concerned, my advice to anyone is to just get to Aswan/Wadi Halfa and sort it out from there. It's really not as hard to sort out once you are dealing with the facts personally.