Let's keep this going then. Same culprit, same accomplice, and they planned to avoid harm to the engine via padding. Either the mechanism inside the base was padded, or, more elegantly, the "deposit" the detective observed on the outside had been replaced with padding or casing that looked similar. This could have created an apparent difference in the size of the engine, but refractive tricks with the glass case were used to compensate.
The culprit was Sir Charles, Jorge as accomplice. He decided that it would be better to risk real damage to the engine than to let his son have it if he lost the court case, so he used the flipping trick mentioned above. It could be retrieved from the base by force if needed later, intact or not.
Killer 1: Akari Junchiro. Signature and motive as I gave before.
Killer 2: Winter. Effectively, this is Fedemon's theory with a different culprit. He once had a sister, who was shot in Naito's gunfight. He is subjecting other people to the loss he felt and getting revenge on Naito.
The culprit was Sir Charles, for reasons suggested above, with Villasenor as accomplice setting off the EMP.
The sides of the glass case were indeed chemically bonded to the base. The base was indeed fixed.
However, the TOP of the case had been cut to create a kind of hinged flap made of glass.
By maintaining a reasonably high gas pressure inside the container, the flap could be kept closed tight. However, once the lights went out, the air pressure was released, causing the flap to fall open, and allowing the thief to reach in and remove the Engine from above. Then, using a sticky material on their gloves, or a suction cup perhaps, they pulled the flap back up to reclose the case. They may have used some adhesive to ensure it stuck, but the repressurizing of the case would have been sufficient to hold it.
Then let's use the story's internal psychological ideas here.
There are two signatures to these killings. We were told by a presumably reliable character that signatures do not change.
Signature 1: A girl is killed who lost a close relative in the war. She is cheerful and popular.
Signature 2: A girl is killed who did not lose any relatives in the war. Whether she is popular is irrelevant. However, a taunting message is left on the body for the detective.
Two signatures mean two killers by the story's logic.
The first killer was Akari Junchiro, who was a huge fan of the novelist Masahiro Junsuke. She envied the popular girls and wanted to be the 'hero', or protagonist. She modeled the killings after the book [The Smiles of Heaven].
The second killer was Entror. He took advantage of the fact that he had a clear alibi for the first set of killings, and imitated their MO to begin a cat-and-mouse game with the detectives, figuring that he was above suspicion. He heard Winter use the term "Mr. Detective," and put that in the notes as a blind. His goal is to prove his superiority.
Edit: Alternatively, I'm just overthinking this and the second killer is Winter, not Entror, who was familiar enough with Seguko's novels to want to match wits with him, openly referred to 'Mister Detective', and planned on revealing that he was gambling with Entror when one of the first murders happened, revealing an alibi that would throw the investigation.
Either way, the love of risks and gambles was a major part of Killer Two's motivation -- the chance to play a game for major stakes.
Similar to the above. However, in this version, Meruko is motivated by the fact that her brother is utterly obsessed by the shooting, and Seguko is obsessed by the unsolved murder. The aforementioned murder-obsessed environment led her to increasingly identify with the books Seguko was fixated with. Hoping to simultaneously act out the role of ‘hero’, in the sense of being a protagonist, and get the attention of her brother and Seguko, she re-enacted the murders and suicide from the novel.
At the age of four, the narrator's mother bought him a murder mystery in which five people are killed. FOUR? Even if he was a prodigy, it seems like a strange thing to give him.
Let's look at the timeline:
1908 - Masahiro Junsuke born
When Masahiro Junsuke is young, his wife cheats on him, has a son. The lover dies in the war later.
~1929 - Seguko born
1931 - Victims all born this year, roughly
1933 - narrator given book by mom
1933 - Narrator's parents killed ("15 years ago")
1941 - "The three of us have been together since we were twelve" -- Zephan, Naito, Seguko
1944 - narrator stationed in Korea at age 15
1945 - narrator returns
1948 - present day (3 years since return from Korea)
The mystery's author is 40 years old. His wife cheated on him with another man when he was young. That could potentially give a kid the age of Seguko or the victims. Let's go with this:
Alibi or no alibi, the students would have become incredibly suspicious of any teacher who wanted to be alone with them after the first murder or two.
However, a student who was well-liked, charismatic, and capable of getting the names of all of Chika's recent contacts?
The culprit is the final victim, Meruko.
Seguko (who she edits for) and Naito (her brother), are absolutely obsessed with murders. Furthermore, Seguko is obsessed with the works of Masahiro Junsuke, and Meruko is the only girl in his life, to the point where he mentally conflates her with the doll-victims of [The Smiles of Heaven]. Based on his writing and subtle cues, she is aware of this.
While in theory her school interactions might give her a respite from this environment, Masahiro Junsuke and serial murders even come up there, as Clair pushes his books at her. This leads to an obsession.
Eventually, she found out - or perhaps merely started to believe - that her mother was Masahiro Junsuke's wife, and that she was the child of infidelity whose existence led to Masahiro's bleak writing. She formed a fantasy in which she was the controlling narrator of [The Smiles of Heaven], making girls smile.
She chose victims to match her age. The "Mom, Dad" lines in [The Smiles of Heaven] suggested that the killer in that story was young, too, and killed "friends."
The "Mr. Detective" notes were an added flourish to get her brother's attention, based on when she heard Winter use the term; it was both a blind and a taunt, meant to deflect attention towards Winter.
In the end, she even did what the narrator of [The Smiles of Heaven] was implied to have done... and cut a smile into her own face.