Wrote what I feel like is a fairly simple machine: https://pastebin.com/Y7Rq6yxA

And yet the game does not recognize it when I construct it in the world -- trapdoor, on top of item input, on top of item output, on top of controller.

Did I mess up the syntax?

I actually got it working by removing the comment line at the top of the file. Not sure why that didn't work, it followed the format of comment lines in the example JSONs.

You can't use comments in json. They're only there for illustration in the samples.

Check your log and see what it says why it's wrong.