If you choose to Top-mount the LCD...
It's not quite as aesthetically pleasing, but it makes machining of the enclosure easier (only a narrow slot for the pins is required) and it allows for unplugging/swapping the LCD.
The provided HLCD 1×9 female header should result in the display sitting on top of the enclosure top panel surface if your enclosure face is 3mm or less. You should measure the ending height of the LCD with the header to assure it will extend the right amount thru the slot in your enclosure. If it needs to extend further, you could raise the header slightly from flush before soldering.
As with the other headers installed in step #4, secure in place with tape
Then solder the 9 pins from the opposite side.
Now stack the pi-Stomp board onto the main Hat Hacker 40-pin header. Seat completely and attach with two screws.
Connect the 3-pin Audio Board Input cable to the pi-Stomp board. Each pin is labeled on each board with “L” for left, “G” for ground, and “R” for Right. Make sure you connect like pins.
Similarly connect the 2-pin Output cable. It only has “L” and “R”, no ground.