First thing I'd do is check the controllers in windows. If it sees them there, then you know your controllers ok. If not try a different port for them and check to see if they are seen then. Once you get past that, I'd do a fresh install of the game if is been more than a couple "updates" since the last time you played. Also, if you may have rolled back to a saved point in windows all bets are off. Restore points can really mess with the game.
You can install the new download over the old with out deleting or un-installing, I think it will update ok. OR, you could save your "settings" folder and delete the rest. After installing the game again just bring in your settings folder you saved for all your head positions and such.
When you have to game installed, go to the map controllers section and use the drop down box at the top to select your stick and begin mapping the buttons. Clicking the "modify" button and then hitting one of the buttons on your stick should highlight that button whether it is mapped already or not. (good way to tell if the buttons work)
Good luck!
