There is a big difference from making your own custom controls and modifying an off the shelf joystick/gamepad.
Look at the restricted parts list. It says that joysticks, etc must use a 15 pin interface. In my mind, this means that you may not use a modified n64 controller.
Ask FIRST, though
Edit: see this thread for clarification:
http://jive.ilearning.com/thread.jsp...9&message=2383