It sounds as if you are dealing with the same issues that we were last year.
We ended up taking a ferry to Tunisia and then driving across Libya and into Egypt. Having met people that did the ferry from Turkey into Egypt, we realized it was much cheaper to do the Tunisia-Libya-Egypt route.
However, there were some ferries running to Haifa, Israel...and we thought about going there and then crossing into Jordan, taking the Aqaba-Neuweiba ferry into Egypt and then continuing down to Sudan. This would require two passports though and our plan for passport stamps would be as follows :
Passport A : stamped out of Europe
Passport B : stamped into Israel, stamped out of Israel, stamped into Jordan, stamped out of Jordan
Passport A : stamped into Egypt
We are Americans and would then have gone to our embassy...or DHL or something and sent our passports with Israeli stamps home. If questioned, we would just say that we took a ferry from Europe through the Suez canal and then got off at Neuweiba.
In the end, we wanted to go to Libya and that option opened up for us and we did it.
I put the passport stamping info in there as that is a way to be able to avoid detection AND have a sensible (albeit unlikely) story of how you got from Europe to Egypt.
When getting our passports stamped, no one even looked at anything but the Sudanese visas...and when getting the Sudanese visas, they didn't even look at our other visas or anything, they were just stuck on the fact that we were Americans and once approved, finally slapped that thing in there.
There are several ways to do it and from what I can see, many of the folks on this forum are extremely resourceful and creative....so I have no doubt that you'll figure out something that works!