I have just come down that way. Turkey - Syria - Jordan (Al Aqaba) - Egypt (Nuweiba). Plan on $100US for insurance etc in Nuweiba. Best option here is to get one of the Tourist Police guys to help you out as I found everything was in Arabic. Took me 4hrs to get out of customs etc, although I was stuck behind a tourist truck. I don't think I paid the tourist-police guy anything, although this may have been part of the $100.
Don't bother with Egyptian Insurance from home as a way to get around some of the above costs. The guys in the overland truck had this specifically to save money and ended up paying, even though they had hired an agent. Most Overland Companies leave their trucks in Jordan and bus or train their people around for just this reason.
I can provide names/phone numbers of agents who can help you across all of these borders. It will cost you though. I didn't use any, but was lucky as I just followed the guy doing the stuff for the overland company in each instance.
See also the post on Egypt Sudan (Share Ferry) for the latest on the Aswan/Wadi Halfa ferry. Good news I'm afraid.