My bad, I just realized that the 3dn files are saved separate of the 3DNes file, but none of the controllers are registering apart from the bumpers (It recognizes then GC controller's start button as a bumper) would it be possible for me to set the GameCube Controller's C-Stick to rotate the display?
Edit: Managed to get the keyboard and mouse to work for SOME games, including Kirby's Adventure and Tetris, but always seem to have up and left held down, also Bubble Bobble is unresponsive apart from rotating the title screen, is it possible that it's mapper isn't supported?