After using the Customization Wizard, and ticking the "Disable all Adobe online services based workflows and entry points", I noticed that on the main screen, Adobe Online Services is still present on the Welcome screen next to Open a Recent File, and also on the File Menu.
In HKEY_LOCAL_MACHINE\Software\Policies\Adobe\Acrobat Reader\11.0\FeatureLockDown\cCloud, there is an entry for both bDisableADCFileStore, and bEnableADCFileStore, and both are set to 1. right. Removing the bEnableADCStore value removed both the Create PDF Online and Store Your File online.
Now I just need to get rid of "Get Documents Signed" as well.