I have not been able to determine Chris's last name either. We are told that it is long and difficult, and hard to pronounce, and that a signalman would abbreviate it. Then we are told that Fr. Chris finds a short bio of "Capt. Cos or Kruss, believed to have been Dutch or German," and that he believes he is "Capt. Cos". However he did not make the connection to himself until he red that Cos made his wife his chief lieutenant.
It is possible to infer from this that Capt. Chris's last name might have been abbreviated "Cos" or "Krus" by a signalman; however, in that case it seems to me that Fr. Chris would have been familiar with that abbreviation, and hence would not have needed the detail about his wife being chief lieutenant to connect the bio to himself. Why Chris would have been mistaken for Dutch or German is a mystery to me, since he told Capt. Burt he was from Jersey (tee-hee), and told someone else he was Italian, or rather Sicilian.
We have every reason to assume Chris's name is Sicilian. He's from New Jersey -- maybe from Newark since he renames a ship "New Ark" (tee-hee again). On the chance that he might be from a real-life Newark mafia family, I looked on Wikipedia and found that the big family there is the DeCavalcante crime family. That's pretty long, but not too difficult to spell and not at all difficult to pronounce. (It's also not at all apt to be abbreviated "Cos" or "Krus".)
All of which is just to say: I don't know.
But while we're talking about Pirate Freedom, I just want to say that I loved it beyond words. I think Fr. Chris has more evil in his heart than Severian the torturer ever had. I look forward to the discussions to help me unravel this Turk's head knot of a novel.
Matt G.