Michael, When you are telling a story, it is conventional to use the past simple to talk about consecutive actions in the past, i.e., the events of the narrative in chronological order. The past perfect is used to tell about the earlier past i.e, events that occurred before the main events of the story. By using the past perfect the writer makes it clear that the events, the letter which HAD been written, the ship that HAD been sailing occurred in an earlier time frame than the events in the narrative. We don't know when this story took place. Maybe he found the letter a month after,in April of 1943. Maybe he found the letter in 2009. The important thing is that the two time frames are distinguished by the reader. This convention of using the past simple to narrate the events of a story in chronological order is well established in the English language. I also agree with fdmaxey that if it is clear that an event occured before another, then it is not always necessary to use the past perfect. Often it is used to reorder the events in the story only for the dramatic effect.

Past perfect is used to indicate some act that was done in the past before another act (also in the past) happened. That is why the past perfect is used in these two cases. In the case of the letter, the act was "being written" and the other act that occurred was opening the chest. The other - Karen sailing on the convoy - occurred before being torpedoed, which also occurred in the past. That having been said, I do not know anybody who would fault you for using the simple past tense in these cases. I understood perfectly when they occurred. It is much more important that the time match. Had you said "Karen has been sailing in a convoy when she was torpedoed..." - this would obviously be a disagreement as to when the two actions occurred. So your statements are not wrong, as far as I can see. Some very, very strict English teacher might say something, but your statements would be understood perfectly by any native English speaker. [Anybody that wants to disagree, feel free. I'd be interested in other opinions]