A trojan is a virus. It's possible that one corrupted your driver. Of course, we have no idea what these "clean up" programs are that you used, so there's no telling what might've happened. In any case, if you are still having virus issues, feel free to head over to our Malware section of the forum for help.
As for your optical drive...I'm not super familiar with Vista (spawn of the devil), but I believe you can access the Device Manager by going to Start > Control Panel > System and Maintenance > Device Manager. Once there, are you able to find your CD/DVD drive? Are there question marks or exclamation points? If you find either of these next to your CD/DVD drive, right click on the drive (in Device Manager), and then choose to uninstall. After uninstalling, restart your computer and it should be reinstalled automatically.