If you are still running Mt Lion, keep doing so and never mind the WD software possibly on your system. Before upgrading to Mavericks, however, doubly back up using Time Machine and Carbon Copy Cloner or SuperDuper. On different disks at that.
Next, unmount and physically unplug those disks. Then download the WD uninstaller cited in this thread, and uninstall any and all WD software/ utilities with it. Then download and install Mavericks.
We have fair reason to believe that after that, it should be safe to plug your external HDDs in again, but do make sure to keep your secundary backup isolated, just in case.
all I see is the virtual CD that I can't get rid of
Try ejecting it with Disk Utility.
I also will be getting another hard drive (trying to figure out the best one will be no easy task)
Any one will do; you never know which of the 4 ( 3 without Toshiba, they only have 2.5" disks and are discontinuing the line ) remaining brands/ firmware of HDDs is inside the box anyhow. Just back up what you need to, before upgrading to Mavericks, and never, never plug it into your newly installed Mavericks Mac until the issue in this thread has been duly resolved.