I took the Visemar ferry from Alexandria to Venice a few weeks ago. Nice, new clean ship, Italian crew, 60 hours in transit, and enjoyable trip overall.
At the time there was no traffic court/traffic police in Alex, since those offices were burned down during the revolution. Only need to show up at the port with your temp plates and the paperwork you were given when entering Egypt. Bring a hundred Egyptian pounds to cover various port costs. It was a very easy process.
But confirm all of this with the contact at the Visemar website when you get to Alex. Things may have changed.