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I got through the first room, but I don't get what about the second room relates to the journal. You've got multiple pages dealing with letters but the only ways of interpreting them I can think of (substitution or hidden messages) don't result in anything.

Sorry. Each page was to do with a respective room (with the occasional looking back for one or two rooms) however pages 2 and 3 got switched somewhere in the process and I didn't catch that I did that until it was to late.  All I'll say is that the third  page has the clues and the first page has the context your looking for for that room.  Hopefully that will help you.