There was an option to go from Saukin to Jeddah. Some friends went that way about a year ago in a Landrover. They got a visa for Jordan in Khartoum, then a transit visa for Saudi, then the ferry tickets then a visa for Syria because aparently you can't get one in Jordan and you won't have time on a three day transit visa in Saudi.
Aparently all the boats going up to Jordan go via Jeddah. Hence you need to get a transit visa even if you stay on the boat and as the roads are supposed to be really good, its probably easier to ride up from Jeddah to Jordan.
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