So, let me speak of what plan I have going forward. In respect to organization, I'm kinda thinking of setting aside a file for each of the main characters to keep track of what topics they talk about, on what days, when they are missing from class, and what-not. These files may contain cut-scenes specific to said characters later, but, the general goal here is to have their dialogs change every three or four in-game days.
Though, if there is one exception to the general plan so far, it's Shoko. The reason for that should be fairly apparent for those who have played any version of this game or the Heartache 101 - Sour Into Sweet custom content pack.