1. With the Deneb USB card, if I install OS3.1, can I just bypass the joystick ports and use USB for everything?
Not bypass, but for Workbench you would be able to use a USB mouse and i guess even a Joystick for Workbench based games. But for stuff like games forget it.
2. Is there anywhere I can send the MOBO to get it fixed?
I think there is a company in France who repairs them.