There's a game about that. It's called Exapunks. You play as an anarchist hacker who is slowly dying to a degenerative disease that turns your flesh into electronics. The medicine to keep your disease from progressing costs 300 dollars a day, so you learn how to hack from a zine and then start making money for your medicine and taking down capitalism. At various points you have to use your hacking skills to reprogram your nerves so your body will continue to function. Send a virus to tell your heart to beat and so forth. The gameplay is based on a modified version of assembly and actual programming puzzles that make sense in the context of the cyberpunk world.

but they just don’t have the reliability I look for in an internal organ

That's ok, neither do regular organs.

I highly doubt The Borg are using 21st century Windows or Linux operating systems.