I've done the Nuweiba-Aqaba ferry independently and it was not a fun time. Tickets could only be purchased the day of travel and good luck figuring out when the ticket office opens. I asked the guy selling the tickets and he wouldn't give me a straight answer. If you can't get on the fast ferry you'll be stuck on the slow ferry which takes a long time to load. I took this and it almost took me 24 hrs from when I arrived at the ticket office in Nuweiba till I got off the boat in Aqaba. Oh yea, there aren't enough seats for everyone on the slow ferry. I saw tour buses getting on the fast ferry so maybe you could set up something from a travel agency in Cairo.

Fly to Amman if you can.