One thing you might want to try to get yourself started on mapping out a customized FPS controller is go out and buy a Raider Pro Joystick, they're about 9.99 I believe, have analog controls (which work in Half Life oddly enough), and are so cheap you can take em apart, do whatever you want to em, 10 bucks is just a meal at mcdonalds now a days anyways.
What I found was pretty fun to do was to hook up my trackball when I had it in a proto-type cardboard box, and hook up the joystick for movement, then use the buttons that were next to the trackball for shooting, and the buttons on the joystick for jumping and action. You could try something portable-ish off of this idea, having a joystick/keyboard/mouse-trackball all in one, but personally I am fine using a mouse and a keyboard when I play FPS games. Having any other controls just doesn't feel as quick to me, (although playing Doom on a controller can be fun since you don't have to aim.)
Also, they do sell controllers with foot controls for Mechwarrior games, I've never used one but I've seen em before, so you might want to just go down to like Circuit City or Best Buy and check out all their selection, then take down notes of the designs you like, maybe even just pick up one of those if you see one for cheap, since that's always the easy way out.
-Good Luck though, keep us posted on progress if you get this thing cranked out
-CthulhuLuke