(Part 1/4, rest is the first couple replies)
-So I never pulled this much from the original game, but in this reimagining I am pretty sure there are strong themes here of gender identity. I know many people have joked about this theory before, but I think there's actual evidence here. The only bathrooms Madotsuki ever enters in YYDD are men's restrooms. To get the secret ending (and to finish the game) you have to activate the symbol of Venus aka the symbol representing female, and then enter into a giant Venus symbol to enter. In the sketchbook there's two pictures you get of Madotsuki that are practically the same, but one with her eyes closed and one with them open. Most related pictures are next to each other in her Dream Diary, but for this one a picture of her eyes closed are next to KyuuKyuu-kun, and her picture of her eyes open is a few pages later next to the picture of the feminine mannequin. Literally eyes closed next to the most phallic character in the game, eyes opened next to the character most with a 'female form'. Add to this the area you get the flute in the mall looks even more like a clinic than the original, and to add to this O-Man's updated look looks a lot more like a doctor, there's character's alluding to genitalia-esque objects on the walls, and E-Man who you go to see in the clinic gives you the Flute. I don't know quite yet on this one if I'm reaching here, but all I'll say is I never got this theory in the original but have it pretty strongly in YNDD.
-I'm going to cover this more in the following points, but I think Madotsuki is a shut-off NEET not because she was raped (I don't think there's evidence for that) or even because of gender identity things. I think it's more straight forward, she experienced multiple scars over the years that made her more reclusive and eventually just shut off from the world. Rather than one traumatic event she experienced several over-time events that made her close off. This also ties in well to unlocking the final door by re-experiencing everything and then when you go out of your apartment having to survive your inner fears (that shadow thing) to get the happy ending.
-Monoko is dead. In the original game the stop/start light changing her form was a bit suspicious and the specifics of the differences, but this remake somewhat spells it out where you can reach her by going to the world end event related to death to find her, and when we see her Post too long. Click here to view the full text.