Display mode stuck

As a very new Mac user I've encountered a problem that seems to be hard to resolve. I installed a couple of Mac G5's preconfigured with OS 10.3.4 and some broadcast editing related apps. We use the ACP output with Apple Cinema monitors. We are also using the DVI output via a DVI to VGA adaptor to feed a VGA to NTSC converter. While trying to configure the second output in display preferences I managed to get the ACP output into a mode where only the desktop background and mouse cursor are seen, all other menus gone. So far we've tried a disk repair, booting from the CD, resetting the PRAM etc. We also reinstalled the OS on the backup partition which did allow the machine to boot normally but unfortunately without the apps installed on the primary partition. So...I need some guidance. I want to recover my primary partition and restore the original display preferences while avoiding a reinstall of the OS on that partition. Any thoughts?