[Ishara]

Are you trying to repair the altar by yourself, or did you talk to the priest near it? You need to talk to the priest, rather than fiddling with the altar.

I didn't buy a ship from a shop owner. I bought it from the dude down on the docks (the ship on the left) in Blackroot.

If you have more problems, there is a walkthrough for sailing to Thanatos, where there are different options:
http://www.gamebanshee.com/arcanum/w...tothanatos.php