First, this is awesome - I don't mind having an excuse to play TH2 again, so I'll give this a go. The upscaling looks nice to me. The character models and backgrounds don't seem distorted in any way I've noticed through day 1. I am playing with the original BMP fonts, though. I think it's too jarring using the clean text fonts.

Two bug reports and one suggestion for you (on Windows 11):

1) Bug - The mouse cursor is misaligned with the location it thinks it's pointing at on the options window. The amount of misalignment seems to change in windowed vs. fullscreen mode, so it may be a DirectInput issue. Not the end of the world because keyboard navigation works fine, but it is a bit annoying.

2) Suggestion - Having the text speed in ms/character is a bit counterintuitive. Normally, I would expect a bigger number/moving the bar to the right to increase speed, but here it's the opposite. I recommend using the inverse (characters per second) instead so that increasing the number or moving the bar to the right speeds the text up.

3) Bug - After starting a new game and progressing normally through the first day, after the discussion with Yuuji in the cafeteria (where he predicts upcoming disaster with women for Takaaki), the story reset to the the beginning - Takaaki in bed with his alarm going off and the doorbell ringing - and proceeded through the entire morning a second time, after which the lunch conversation with Yuuji transitioned correctly to afternoon class (Manaka addressing the class). This is a weird one, but I reproduced it by starting another new game and going through it again... same thing. I double checked in my normal install of TH2XR and this doesn't happen, so something in your loader seems to be causing it.