1. The thing why it's happening, it's because mod author decided that he don't want to alter part 1 much, and it's still on middle if you just look at the "square" that is the same size as original MG version, so it's in middle there. Technically I can make it so the story would appear like in part 2, so background on full screen and box in the center. But I'm not really sure if that would be good, honestly you are first one to complain about that.
2. Probably yes, but nobody bothered or atleast I haven't seen complaints about that too.
3. You can access it the same as in part 2, in owari...
View attachment 4789916
and in new version it will show from menu
4. From that I know she is only one that cannot be cleared, don't know why mod author decided that these characters are like that in this mod, but hey it's mod, but people still play it like it's original game lol. But anyways if you think of some solution( maybe add to NG+ part 1 points to get her at the start game or something) I can implement it, at the moment it's just a state of translated game with "few" additions of our translation-development team.
For complaints about the mod you should complain to original jp mod author, tho he didn't answer on twitter or anywhere and not making further updates to the mod, so it's probably pointless. We just translated the game, but future update (coming soon) will add new content, and we plan to expand it further, so suggestions are welcomed. Can even change some annoying things that mod author did.
And for the ID question, if you open cheat table you can see every character ID.
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It's in Unit Editor, right click identifier, set/change dropdown selection options.