I can only echo the comments above: Time Machine is a better way to create backups for your MBA, it also saves you loads of room on the portable drive as it backs up incrementally instead of creating loads of duplicate files. Switching to that will also solve your access issue as you won't have to copy the USER folder anymore. As far as I know you cannot use Time Machine to revert your whole system back to a specific point in time (that's just a silly Windows approach to solving problems).
Just a thought, but the fact that you're still running Mavericks may put you at more risk than what you're trying to prevent through using Sophos. Also, the issues you're having with that may be related to the age of the OS. If Sophos has updated itself it may be out of tune with your OS which could account for the scanning issues. Updating to a more recent OS version could be the solution to that problem.