Hi JulieBuny,
I did a Med tour this summer.
My route was : Tunisia, Libya, Egypt, Jordan, Syria, Turkey, Macedonia, Albania, Montenegro, Croatia, Bosnia, Slovenia, Italy and then back to home in France.
I took a ferry from Marseille (France) to Tunis (Tunisia), around 300euros one way with the bike, no cabin...
Entering Tunisia takes 10min, all the paperworks are done on the boat. Just had to declare my GPS at the customs but if you hide it it's ok you'll skip that.
For Libya I asked for a transit visa. I repeat, a TRANSIT VISA. I had to ask for it at the Libyan consulate in Marseille (France). I had to get my passport translated in Arabic (45euros, in cash of course...) by the official consulate translator. Then I had to fill some forms and I waited around 4 weeks. When it has been accepted I had to go to the consulate (they don't send it by mail) to get the visa on my passport. Pretty expensive... 80euros...
So I entered Libya WITHOUT A GUIDE, ALONE. But I had to stay on the coast road, not allowed to go south without guide. I had 2 weeks to cross Libya. I had to leave a deposit for the Libya license plates, I got it back when exiting the country (minus a small tax).
For Egypt I got the visa at the border (around 12euros) then I had to do all the paperworks for the bike, boring... it's a terrible mess in Egypt, quite crazy. They asked me 80euros for all the paperworks, 5 euros here, 10 euros here, 3 euros here, etc... you pay for everything without really knowing what you're paying for. I had only 50euros so I had to leave the bike, enter Egypt with a truck driver, go to a bank, get money, find a bus to go back to the border, finish the paperwork, and then after 26h I was allowed to enter Egypt with the bike. Don't do the same mistake, takes a lot of euros or dollars! If you can try to find a tourist cop (white uniform) who speak a bit of english and ask him to show you the way to the differents office, etc. Most of the time they will not ask for money for that service (that's a miracle in Egypt!).
I spent 4h to do all the papers to exit Egypt in Nuweiba... then I went on the Nuweiba/Aqaba ferry. It was 8h late so I arrived in Jordan at 1am... border crossing in Jordan was easy, around 30min and 12euros for the insurance. There is a camp site 10km far from Aqaba along the red sea in direction of Saudi Arabia if you feel tired after the boat trip.
For Syria I had to apply for the visa before leaving France as they don't deliver visa at the border (even if some guys managed to get one). It's better to get it before so that you're sure you'll enter the country. It took me around 1h and 20euros (IIRC).
For all the others countries it was easy with a Euro passport.
I forgot to say that I had a carnet de passage for the trip. Maybe you could do it without but it makes things really easier...
I hope that help! Feel free to ask if you need more informations