E drive disappeared, but CD/DVD device is still detected and sort of functional...?

Run a system restore back to a point in time before you tinkered with the registry. It may resolve the issue with the cd drive but you may also have the spyware again. This time instead of messing around with the registry yourself let a program such as malwarebytes do the job for you. Sometimes programs such as Roxio or Nero can mess around with the cd drive as well. If you have the installation discs of these try uninstalling them also to see if the issue is resolved. Finally you could try changing the drive letter form E to something else up the alphabet in case the drive is conflicting with some other device igning the same drive letter.