This is inspired by Realities' excellent idea, but I used a PC controller instead of a keyboard circuit board, eliminating the need for an elaborate flipper build.
Take apart the guitar and gut the electronics. Lots of good stuff in there for other projects! Remove the frets and cut the wires from the frets as close to the guitar's PC board as possible. Go ahead and take apart your controller as well. If your controller has Force Feedback motors, you can simply snip those off without effecting how the controller works.
Trim plastic on the guitar body shell as necessary until you can nicely flush fit your controller PCB into the guitar body shell. You'll want to fit it at an angle with a multiple of 45 degrees (i.e., 0, 45, 90, 135, 180, 225, 270, etc.). This makes use of the eight way position of your controller's joysticks, so that two of the positions will be "up" and "down" for the "flipper" picking used by the Frets on Fire game.
Use a circular file or Xacto knife to make a whole for the controller cord. I found that using some hot glue around the cord just inside where it fits in the guitar body makes a nice "stopper" to protect the cord from being accidently yanked out, just like the rubber stoppers used on regular controllers. Now, reassemble the guitar. Almost done!
Your controller is perfectly usable at this point, but you can do some cosmetic work if you want your controller to have a "finished" look. Thin 1/16th or 3/32nd aluminum sheeting can be used, as it is easily cut, even with scissors. Plastic cut from coffee can lids, cheap tupperware, etc., also works great! I used colored tape on the frets to match the color scheme used in Frets on Fire, and hot glued two extra thin guitar picks to the flipper controller. The real beauty of this is one joystick becomes the flipper, and the other stick allows you to navigate through all the game's menus from your guitar!
Have fun with your new controller. If you'd like to support this Instructable, and see my controller in action, then please watch the video! Thanks and have fun!
Watch the Video!