Step 9: Pack it Up, Pack it In
This is the part that is going to be the most variable, depending on what sort of cavity your guitar's body has. It's also the part I've spent the least time on, so if you're an enclosure master, let me know, and we can make this better.
If you're willing to cut into your real guitar's body, that will probably let you make the guitar look much nicer than mine. However, remember that even on an electric guitar, the size and shape of the body have an important impact on the sound of the guitar, so if you're going to want to play it for real again, you might not want to make any big cuts into your guitar.
You'll probably want to cut out the strum bar from the plastic guitar and mount that back onto the board the controller is on.
For now, since I'm not currently using their features, I cut out the whammy bar potentiometer, along with this switch that doesn't do anything for the controller. Then I found where things would kinda fit, and through a combination of wedging, cutting, and screwing, I fit things more or less into the body.