If you're in Khartoum and want to avoid Egypt, the following might be helpful. This was our route last summer.

There is a shipping agent in Khartoum - Baabud Ferries ticket office on the intersection of Al Hurriya Street and Zubeir Pasha Street. (Not too much english spoken there.) There is a big tattered ad of a ferry on the outside wall - the office is through a hall and up a flight of stairs. But we subsequently discovered we could easily have driven to Port Sudan and bought our tickets there. Tel: 0183 774233/797212 (They may have a Port Sudan office and number.)

We got our visas for Saudia Arabia and Jordan from the embassies in Khartoum.
There was some talk about Saudia Arabia not accepting right hand drive vehicles - in our experience, that isn't true.
There may also be an issue about women who are single and traveling without a husband or brother. You'll have to check that out and work round it.
Sorry - in view of the hosts of this site, Saudia Arabia wouldn't accept bikes through their country.

Failing that - in our experience it was worth splashing out for a night or two at The Acropole Hotel and meeting the greek brothers.I've not come across a more helpful pair of brothers. They are very well connected in Khartoum.

Dear Pindoria and others,

Considering the current situation in Egypt we are looking into getting back to Europe via Saudi Arabia. Could you please provide the contact details of the 'Greek brothers' so we can get in touch with them?

We would love to hear any other suggestions on how to avoid Egypt but still getting back to Europe.

Thanks!

The Acropole is great. Here is their website.

Acropole Khartoum Hotel Travel & Tourism

The brothers names are George, Makkis, and Orthanakos, I believe. They helped us out a lot as we were trying to get to and then out of Khartoum during all of the embassy attacks last September.