James, regarding whether there is any SciFi media about harvesting humans for body parts, there is a video game from the 90s which has that as its main plot point: Xenogears. I'm going to spoil the story, so if anyone wants to play the game for themselves they should stop reading now.
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Basically, in the world of Xenogears it is revealed that humans were actually genetically engineered 10,000 years ago by a sentient, biological WMD named "Deus" (or "Yahweh" in the JP version) who, having gone into hibernation after having sustained severe damage, created humanity with the goal of harvesting their body parts at a later date, once enough humans would roam the planet. Throughout the story, the protagonist discovers that the entirety of human civilization is nothing but a "Plantation System" run by a hidden nation living in the sky: Solaris. Solarians were "chosen by God" to control the human population (whom they call "Earth-dwellers", "Lambs" and "cattle"). Throughout history, when humans were considered "unfit" to become the "spare parts of God", they were genocided by Solaris and human civilization was restarted: this happened several times. Once you get to explore Solaris in the second half of the game, you discover that they've been abducting people from the surface in order to either experiment on them (creating some frightening abominations) or to process them as food in an aptly named "SOYLENT" facility.
In the final section of the game, Deus awakens from his 10,000 years long slumber and LITERALLY ABSORBS THE ENTIRETY OF HUMANITY. Except for the heroes of course, who manage to defeat it.

Xenogears' story also deals with lots of other subjects, from nanomachines to gnosticism, from mind control to Jungian psychology, from forced vaccination to the evils of organized religon. It's basically a tour de force touching on every possible conspiracy theory, but instead of playing it for laughs like it's usually done, it's actually a pretty tragic tale (even though it has a happy ending).