Thank you for the tip, and sorry if this wasn't a good place to ask, but you helped a lot and I figured it out! I was running the "online version" of the hack, which had different installation instructions. After reading the instructions for the other versions, I put the files from the zip that went in the "Luma" folder into the extracted romfs folder of a dumped version of Pokemon y, loaded it up on pk3ds, randomized it, and then built it back as a cia file which ran fine through fbi.
Thanks for the help!