JK2 nowadays comes already patched to 1.04.
In order to play with us, you should use a version switcher, an easy non-destructive tool to quickly jump between 1.02 and 1.04.
Extract this inside your GameData folder. It can be found where you installed the game. Then run the JK2vs.exe and follow the instructions there! This also works on the Steam version of the game, and the path is by default -..\steam\steamapps\common\Jedi Outcast\GameData.
The tool comes with separate folders for 1.02 and 1.04, and keeps the original files there - then it simply switches out the necessary pk3 and system files for it to work on either version.
If you find that your controllers have lost their key bindings after such a switch, try to execute any configs if you have saved any. If not, you could always go to Setup > Defaults, and it will set all controllers and settings back to default. See here for more information on setting up your game settings.
EDIT: Discard all above and get www.jk2mv.org