I think I have a bad or corrupt HDD in the controller. The controller won't boot up. I connected a monitor to the video port and saw a message saying something about an unrecognized boot device. What options do I have with upgrading the drive with an aftermarket drive. I know I will need to get the software some how. Any suggestions?

Call tech support. You can send the drive back to New Jersey and they will ship you out one with software installed. I think they need to know if its the old or new version.