By removing the following registry key, the Libraries will be hidden from the navigation pane and when launching via Win + E, Windows Explorer will default to the virtual Computer folder. If you apply this solution along with @Qwilson's then it should take care of everything except for launching from the Run prompt.
After you delete the key, you may need to log off, or restart before it takes effect.
In order to take care of running from the Run prompt, the only solution I could find would be to change your habit from typing
explorer to typing
Note: I also found it very helpful to have the Homegroup feature and services turned off. When I tested this in a Virtual Machine with the Homegroup feature on, some launching methods would default to selecting the Homegroup.
In Windows' Run command line, how to open "My computer"? (@paradroid's answer)