YOU CAN NOT GO AS A FREIGHT SHIP PASSENGER TO EGYPT, the Egyptian authorities do not allow neither embarking nor disembarking from freighters by passengers. One way is to go by train from Istanbul to Halab (Aleppo)(through sleeping car once a week), from Halab to Dimashq (Damascus)(daily), from Dimashq to Amman (Mondays and Thursdays), by taxi (or maybe bus) to the Aquaba Bay and by ferry to Egypt across Aquaba.
But can you go to and through Saudi-Arabia?! You will hardly get a tourist visa for individual travel through that country.