I couldn't agree more with you. The Room with Clocks and Ami melting scene were at most gross and delusional. The Town has Two Halves made me sick in a complete different way that never had I ever thought before. It's not just the MC is the cause of all the horrors and regret. But also the story is predestined and doomed because of you from the start. The scene flashed "You can not choose", "You have already made your choice" with the glooming melody of Blue Air (God I love it, I really appreciate how Sel unearthed this heavenlytreasure) and it made me so sad. Forced and entranced me to watch each line and rollercoastering straightly to abyss. To be honest I'd list it above The Stomachache since we suffered too much at that point and could still do a better choice.
Another thing that almost made me uninstall the game was, you guessed it, The Bluejay. Literally I wanted to jump into the game at that moment and put a bullet in his head when he merely said "I'm feeling particularly callous tonight" after so many red flags Makoto showed. I knew Akira became more and more human-like and tender as the game went but gosh he in the Chapter 1 was a completely distasteful sex machine in human skin (new Maya feels also so).
I want to add Lavender's Green, but not particularly for its horror or shock aspect, but how real this scene can be.
while This Town has Two Halves and Bluejay work very well as they take place still rather early on in the story, Lavender's Green is almost at the end of Chapter 2, so by then you know the game is not nice to you. what does feel horrible is knowing Molly drinks, she just had her heart broken, and Sensei being a terrible person who already preyed on the other girls before, be it willingly or not. mix all of those things together and you got yourself a recipe for disaster, that you know will most likely happen due to how unfortunately common this scenario is in real life.
the fact we don't know what happened at the time is also both horrible and a blessing in disguise, as I wanted to keep reading to satisfy my morbid curiosity, (even if the answer was either "bad" or "really bad") but really coming close to quitting. it was also one of first event to initiate a first step towards Akira regretting his(?) actions and bettering himself (I could also mention how this plot point was the first to ever make Akira show emotions toward us -the players- and one of the girls, its lasting impact on Molly's relationship with him, etc... overall a very "make or break" moment)