Where's the post? I can't see it from the letters.
Yeah, the 3DS version is the ultimate version where they added the best sprites, remastered the music (which is awesome btw) and added missing scenes that were missing in the PSP version (the PSP version was incomplete as the chapters were still being written, but they released the game anyway)
Wrong ends are collectabes in themselves (as you get a checkbox for each you see). The notes that lead to an end is a one time gimmick, it's just that one that taunts you to collect them despite even warning you it will lead to a bad end lol
Same with name tags, they're collectables just to see how many people were lost and in what ways (You had the monokuma figures in DR2 for example) And well, yeah, no specific way to tell what you missed, you just save and explore, and if you trigger a cutscene, you reload and explore the other path, otherwise you can go to any chapter at any time to see what you missed. Most of them are extra so even if you miss them, you just lose curiosity points. Later chapters do trigger "best"/"worst" ending based on what you saw tho.
Flies... well, you could argue some came aboard with the students and then nature took over. Plenty of food for them.
As for dimensions, I can tell you, but it will be explained later. Let's just say those people have been there for a LONG time.
As for endings, I there is a list of endings in the settings/extra menu so you can see how many there are per chapter (if there is only 1 listed, then what you see is what you get, I think the "good" ending is a bigger circle).