If you don't get the N64 controller to work you may want to try a wireless xbox360 controller with the usb wireless adapter. Every key can be mapped on it. I use this with a mouse at the same time. Mouse is used for looking around, shooting, reloading, opening doors, changing weapons and the controller for moving, aiming, jumping, ducking and the rest is mapped to the buttons and d pad. You get the precision of the mouse and easy movement with the stick. I've been playing this way for years and years. I think its awesome but I'm sure other people prefer their keyboards and mouse. I also have that kontrolfreak stick extender which is nice.
If you recall the original game had an option to use two controllers at once which is similar to my style.