Sounds like you did not do a clean install or update the hard drive drivers. How did you install OS 9 if the CD drives do not work?
Did you try restarting and holding down the space bar to get the extension manager?
Don't give up. First, insert the OS 9 CD in the USB drive and do a hard restart -> command(apple) + control + power key.. then hold down the C key. If that does not do it, try it - restart then hold down Delete + option + command (apple) + shift. This will force the computer to search for an operating system other than the hard drive.
Once you get the computer started with the CD, open the Utility folder on the CD and run disk First Aide. Have it verify then repair all the problems. Then quit that. The drive icon should show up on your desktop when it is done. Open it and check to see if you have two system folders. You only want one. Trash the other if you find two.
Open Drive set up and go to the menu and select Update Driver. Quit that, and open the installer. The second screen will give you either an options button or a box to check. You want to select perform a clean install.
The clean install will create a new fresh operating system and rename the old one previous system folder. Now you need to install your drivers for printer, etc but I highly recommend that you download the correct updated drivers for OS 9.
Keep us posted on how you do and if you need further help.