Happy New Year to you too! It did indeed take me some time to finish Ren's fight scene, and most of it was done in Photoshop.
About your questions:
Ren means "lotus" in Japanese, while Inei means "shadow/shade." I won't tell you the exact reason Ren decided to use those nicknames, but their symbolism might give you a clue.
I explained it in Chapter 4, but yeah, as uniforms keep changing, I don't blame you for getting confused. White uniforms are for the butterflies (students from healthy families), gray is for normal students, and black is for Shugosha.
The first design is cool but inefficient. I already explained why it's a bad clothing model, but to make it short, it doesn't follow the character's physique and is very limited in movement.
The uniforms are meant to give a noble feeling as this is a private academy. The sailor uniform was an error, as I forgot that it's still a winter uniform for the students.
The intention for the "???" section is a secret.
The first one can't be accessed if you decide not to tell the truth to Inei in Chapter 4; in that case, he will speak with Akira. The second one is, again, as I mentioned in one of the comments, "Finish the game with perfection and imperfection."
Mirai is truly a goddess, and yes, koalas are very cute.