Issue with folder permission in file server migration - Share Parmissions VS NTFS Permissions

I am migrating a file server form 2003 to 2012 R2.

There are about 50TB of files with thousands of individual permissions.

I have successfully migrated the files to the new server, including their permissions which remain intact.

I am having problems with permissions.

Lets take the Accounts folder for example: On the old file server, it is shared with the permission: Everyone Read The NTFS security is set to: Accounts Full Control Finance Read & Write

This results in users being able to see the shared folder Accounts but not accesss it or view it's contents unless they are in the accounts or finance groups.

On the new 2012 server, i got to advanced sharing, add the permission for everyone to read, and create the share. I then check the NTFS permissions for the folder, they are still intact, Accounts, Finance, thats it.

The problem is, everyone can read every file in that folder. It appears the share permissions are taking precedence over the NTFS permissions.

The same thing happens on the 100+ shares on the new server, it is not feasible for me to manually re-do all the permissions.