The guide is not laid out in chronological order, as it's not played that way. Although the guide goes from one page to the next, this is not a suggestion for the order in which you should play. To make the most effective use of the guide, navigate to the page concerning where you are in the game from this page or the table of contents.
Some of the level events can only be activated after you have the second mission objective (MO2) available for completion, for example, the floodgate at Kyoya Day 1 - 08:00. This is very common. Your usual guideline for knowing what's possible and what is not is: if a part of the level has something to do with MO2, it won't be accessible/useful if you only have MO1 available for playing/completion. This are not mentioned during this guide, and if you're a new player you probably won't know what's like that and what's not, but hopefully you can deduce it.
Some of the level events can't be activated if there's an alerted shibito nearby. The game says "There's no time for that right now." and prevents you. These aren't explicitly pointed out either, so if it happens to you, remove yourself from the shibito's notice and try again.
Spoilers are inevitable and in great abundance within the guide, so know that before reading.
When a lesser objective is listed as "not mandatory," it means that you can skip doing it and still pass the game. However, there may be some consequences which make your game harder or more frustrating, so if you're not sure, you're better off just trying to complete them all.
Not everything is mentioned about every mechanism or item, etc. - only the things that are of practical importance or are somehow more interesting than usual.