In order to better envision the issue, since your written explanati9n is good. enough, could you please upload some examples of the "extracted Mystic Square 's images data alongside the jumbled/failed of the edited custom-fojt (ZUN.COM)
Thank you in advance.
ZUN.COM looks like this in yy-chr
I think it is an executable rather than a custom font, but I am not sure. The other .BFT files display this
I didn't edit them so nothing in-game has changed, but it looks like the dialog text uses the system font (FONT.ROM). I was editing the wrong half of it so I made a small change to test it.
What I can't find is the sidebar text (bombs, players) and the font used in the menu. In Touhou 2 these were stored in mikoft.bft