As you close the case, use tweezers to poke the wires around inside so that they do not interfere with the standoffs.
We wanted to make sure we could update the code without going through the disassembly process, so we drilled a hole in the back right over where the button is, then used a paper clip to push the tiny button. You can also just solder two wires to GND and RST and bring these out of the case, when shorted it will start the bootloader.
You're done! Enjoy your new toy, and modify the sketch if you need to change the key commands or mouse movements.