I have a question that's completely unrelated to the plot: On page 32 it says that both Momiji and Kouyo are written the same? How does that work, both in terms of how are the same characters making such different sounds and how would someone who's reading it know which set to use? Is there more to this that I'm missing or that isn't coming across?
I remember asking a Japanese tutor about something similar a, very long time ago, but I couldn't think of a good example at the time, so she wasn't able to give me an answer and I didn't stick with my studies well enough to figure it out myself. (I really do need to go back and work on that.)
When Japan adopted the Chinese writing system, they were faced with a problem: Japanese and Chinese are extremely different from each other. The solution they came to was, alongside adopting a number of Chinese words (whose pronunciations were suitably changed to match the Japanese syllable system), to also use the Chinese characters to represent completely different Japanese words with similar meanings.
As a result of this, most Japanese kanji have both a kun'yomi, a Japanese reading, and an on'yomi, a Chinese reading. Indeed, they frequently have even more than 2 such readings. 行, for example, has at least 7 different pronunciations, ranging from "i", "yu", "oko", and "okona" (kun'yomi) to "kou" ,"gyou", and "an" (on'yomi).
The case in question is actually even more complicated than this. "Kouyou" is the on'yomi reading of the kanji compound 紅葉, but the "momiji" reading actually derives not from the individual kanji in isolation but is a reading that only applies when they're both used together.
As for how to know which reading to use, unless the writer provides the correct reading in tiny characters above the kanji (called "furigana," which you may have heard of), you have to rely entirely on the context in which they're used.