Im a little confused as to what you are trying to do. If you say that the bulk of the data doesnt riside on the WHS shares then why are you looking at the D drive of the WHS?
Where is "the bulk" of your data actually stored then?
If Keepvault is already backing up your WHS shares then the data in your shares is protected.
As for bare metal restores, if you are only backing up the shares then your computer backups are not being stored by Keepvault and so if you would also need to backup your computer backups.
More information on how to do this is in the Backup Technical Brief which you can find on
http://www.microsoft.com/windowshomeserverAndrew
MVP - Windows Home Server