The only info I have is sketchy, to say the least, and you shouldn't rely on it too heavily. However, as no-one else has picked up this thread I'll add what I can.
There are no ferries to Jordan except the one from Nuweiba, Egypt. I'm not sure about ferries to Israel but I very much doubt it - and anyway you won't get through Syria if you've got an Israeli stamp. So your realistic options are container or some sort of locally-sorted out dhow.
I would think that Djibouti is better for containers but I haven't been to either so don't take my word. One other option once you're going down the container route is to look into shipping to Egypt. Again I don't knwo much about it.
Re: Syria, I think that you can take a car in without a carnet, and I think that some nationalities can get visas on the border. However we had visas and a carnet when we went through so I can't say first hand. The requirements change quickly, and we went through a year and a half ago. We did meet some French people who had got through without carnet. You will have to pay $100/week Diesel Tax for Syria, which is an arse.
May be worth trying to contact some of the overland trucks, either in Addis or via their websites to see which way they go, as I know a lot of them have to go by ship down the Red Sea. Don't know if they use different vehicles at each end or what, but they should be able to give better advice than me.
Sorry it's all so sketchy!