I've added a better custom controls setup. It should work with just about any controller or joystick ever. If it doesn't, email me at 'michael at michael todd games dot com' & tell me the details so I can fix it in my next patch.
It will (should*) work by default on windows/OSX/Linux with keyboard or xbox360 controller. A ps3 controller will need you to go to the controls menu (just press ESC in the main world area & select controls, or walk to the controls computer), and select 'Set Player1 Controls'.
As with any complex new system, there are bound to be bugs. I've tested as much as I can, but at some point, I can't find any more & have to just release it. If you have any problems, please email me at the above email.