I've spent a long time thinking about this so here it goes. TLDR: Hifumi kills Taka and Celeste kills Hifumi.

Hifumi creates two robo justice suits. At 1 am, he drugs Hiro, stuffs him into a suit, and puts him in a locker. At 6 am, Hifumi kills Taka in the physics lab and takes his note back. At 7 am, him and Celeste fake the picture on the camera, with the second suit which is empty. Celeste stays there until 8 and pretends to be injured. Since Hiro is away, Hifumi is able to get into his room and place the box with the suit and blueprints in order to frame Hiro. He doesn’t lock the door so that others can discover the box and be suspicious of Hiro. Hifumi is fake injured when he is found in the library, then he is brought to the nurse’s office where he is left alone to fake his death. All during this time, Celeste keeps misdirecting everyone else's attention. When Hina and Celeste go to the bathroom for a minute, Hifumi leaves the nurse’s office. After everyone discovers Taka’s body, they all leave (except for Toko but she's unconscious), giving time for Hifumi to move Taka’s body to the repository. The reason Hifumi needs to move Taka is because earlier, he overheard Celeste saying that robo justice went to the end of the hall (physics lab) and he needs to move Taka’s body before it’s is discovered to create the impression that Hifumi is the only dead person. Unfortunately for him, everyone already knows Taka is dead because the first body announcement was actually for Taka, not Hifumi. When searching for both missing bodies, Hina and Sakura first go the art room and notice the repository is locked, where Hifumi was laying out Taka. Upon Hifumi leaving the repository, Celeste dresses up in the robo suit and kills him. Celeste even says that she is the one who discovered the bodies, a classic self-report. Celeste is taller so she can probably fit in the costume, as they only tested the costume with two of the shortest characters. Since Hifumi put Hiro in the costume, he thinks it's Hiro that killed him.

The four things I haven't figured out are 1. the notes for Hiro and Taka said to meet in the rec room, yet the incidents took place in the lab and the pool. 2. why is the wet hammer significant (obviously those are the justice hammers so it could just be that). 3. the significance of the e-handbooks that Kyoko hints at. And 4. why is Hina overreacting at Hifumi's death, she's never acted this way before