Here's what I think:
The puppet is most likely male...because it has the rapist's penis. Of course, as I explain below, there's still a possibility it's female.
The puppet will have the MC's memories, two identical arms, two identical legs, the fat guy's viscera, the little girl's heart, Arrowhead's brain and head, and of course the rapist's penis. Or rather, it will have six of those things, since one of the aforementioned people is a puppet.
Of course, seeing how fucked up the story is, I'd wager that the little girl without a heart is the puppet. Because Japan just loves girls with male genitals (the rapist's penis). The problem is that we see the little girl at the beginning when the two kids are talking about all the students who go missing. My second guess is the main character. They already kinda shot that one down, but it would make an interesting plot twist if he found out that he isn't even a real person and that he helped the others for no reason. Thirdly, I would guess Arrowhead. He is always doing something on the computers. Of course, he could be hacking to find a way out for everyone.