How to upgrade hard drive on Mountain Lion Server 10.7.4 ?

I was trying to upgrade my Mountain Lion Server (10.7.4) with a new hard drive. I copied over all the files from the previous 500GB DATA hard drive onto my new 1TB DATA hard drive. All admin users were able to use all the files with the new hard drive attached to the server. All my "student" users did not have permission to access documents, desktop, downloads, etc.. Because of this, they are not able to use Google Chrome or Microsoft Word/powerpoint.

Whenever I click on Chrome, it says that "google chrome cannot read and write to its data directory".

I tried to change the permission under shared settings in the server app. But it does not help.

I am upgrading my hard drive, I was wondering the correct way to migrate my data over onto my new hard drive.

How do I upgrade the hard drive on the Mountain Lion Server 10.7.4 the correct way?

Thank you in advance.