You must also replace the CR2032 battery on the back plane. That may be the source of the Fatal Fault. Following battery replacement, you must do a clear. There are plenty of YouTube videos on doing a Ram clear on the S9000. That's the easy part. The challenge you face is restoring all the machine/game settings. Not an easy task if you haven't done it before. You should be able to find YouTube videos on that too.
For the 326 OS, I believe you need a 320 clear card.
Once you change the backplane battery, clear and reinstall the game settings and get it running, you can further troubleshoot if necessary, as your original problems sound like something more than just a low battery. Whenever you have a problem, be sure to look for an error message.