Forget playing the game for now.
Firstly, let's turn off the hardware acceleration, then reboot the game to establish that the mouse cursor problem is down to that (which I'm sure it is). If the mouse appears when hardware acceleration is off, you've found your problem.
Secondly, as you don't know what command you are looking for in the config file (I can't remember because it was so long ago), you will need a file comparison tool (Windiff, CSDiff, FCU).
When hardware acceleration is turned OFF, make a copy of the config file to a temp location. Then go back into JK and turn ON hardware acceleration.
Save the changes, come out of the game and make a second copy of the config file, place it in the same location as the other, but remember to save it as something else, DO NOT overwrite the first file.
Do a file compate to find the differences in the two config files you copied. Play about with the field(s) that are different, and see if you get lucky.