Each chapter contains a cipher. Chapters 2 (Admittedly “Cipher” is a bit far for this one, but it’s a hidden message) and 4 still have unsolved ciphers.
I’ll give a clue for chapter 2, in one of the C1 sources, I’ve hidden instructions on how to solve it’s puzzle. Chapter 4 may take a bit more work, but clues are hidden in there.