To find the sunken city, look for the old broken down cart in a small spot on the west shore of the Lost Sea. Then head due east, watch for your icon to take about 30 steps and you should be close. The map made a kind of metalic clunking noise when I was above the city. I don't know if this was a bug, a something that happens only after you get the Treasure map from the old Pirate.
After you Raised Anephas, there is a door that is now open in a passage to the right of his altar. That takes you to the Lost Sea. If you didn't go this way you've been looking in the wrong Sea.
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