I agree! Now, this is entirely up to you, but you said that you already somewhat altered the original narrative anyway, so maybe you can fill in the plotholes either yourself or with the help of some other people. Although I understand if you don't want to do that.
I only really made the tiniest of tweaks though, like in the original CD, Kakeru refers to the listener as "sis" a hell of a lot x3 Which I know is fairly normal for Japanese stuff, but it just wouldn't work in my version where I let players pick pronouns, and I've never been a fan of that creepy sorta stepsibling romance trope either, so I used the opportunity to just change him referring to the player as sleepy, or by their chosen pronouns instead, haha.
And then there's the scene where they have their little fight. In the original CD, the jump to the next track/scene is really quite jarring, and since the listener would go on to choose who they ended up with by deciding which final track to play, I figured I'd put the choice in-game directly after the fight scene and write some accompanying original dialogue for their reactions on who you side with. It would've seemed a bit strange to make the player choose someone and then just move on without a word, haha.
That's about it though for what I tweaked :3 The rest is all true to the original.
It certainly would be fun to play with it all a bit more, but yeah, I don't feel all that comfortable writing too much content for characters that aren't mine >.< So I'll probably just stick to localising without messing with the story too much. I don't really have the time to dedicate to adding original writing to YH either cos I need to make progress with DD since it's been far too long. I promised myself and anyone following the project that once Yandere Jam was over, I wouldn't participate in any jams or work projects other than DD until Spooktober Jam rolls around in September x3 cos DD has been on the sidelines for waaaay too long.