Forget the boat, no boat at the moment..!
Unless things would have changed radically, there's no ferry service coming to Egypt for the time being. At best a RORO, with a number of complications. I submitted a number of informations on other threads, please do take the time to dig and find. I'm in Egypt at the moment and trust me this is not a simple country to enter a car in even with privileges, I actually fear the day I'll be getting it out. Same for the bike, not simple, and expensive, but wow, what a place to enjoy when you're out there on dunes.
In a nutshell, just do it! Provide the deposit they ask, it's worth it as it's a deposit only and not a tax unless you screw up right. If Egypt is above availability of budget, I'd suggest to sail to Port Sudan if possible, or even further to Djibouti and then enter Ethiopia. You can also sail to Mombassa and drive on from there. The choice is yours, so consider entering Egypt but I'd recommend to plan for serious fun time traveling the country to cover for the extra hassles...and there are many..! Enjoy.