30 out of 60 GB available. So I went into root. Renamed the exisiting library folder to lib.old. Put in the library folder from the backup package and rebooted. All seemes normal with the world now as the prefs seem to be good.
Let this be a lesson to those that dont back up...
Edit: What I cannot figure out is why MessageSorting.plist was not in the backup archive? This is the file that contains all the rules for Mail.app. Great, now I have to recreat all my rules.