That being said, I feel like the long pins being on the side they are after the install is preventing my board from sitting where it should in the case.
I'm hoping I didn't install them incorrectly. Reading the guide:
13. Insert the 40-pin header into the Raspberry Pi Zero long pins first then solder the long pins starting with one pin in each corner
That seems to make things too high. See the pics.


The board sits much higher at the top of the gameboy than the bottom.