In your case, i would use Migration tools that are included in Windows Server 2012 R2. It will migrate everything (shares, permissions, data...) and it's a full supported way to migrate from Windows Server 2003 to a newest operating system. Last but not least, it's very simple to use it.
Basically the process will be the following :
- Install a new Windows Server 2012 R2 VM with all needed VHDs
- Install File Role and Services in the new WS2012R2 VM
- Install the Server Migration Tools on destination Server
- Open TCP and UDP port 7000 and make sure that it is not in use by other applications. This port is used by Send-SmigServerData and Receive-SmigServerData to establish a data transfer connection.
- Verify that the destination path has sufficient disk space to migrate the data
- Use the same drive letters for the destination server volumes as for the source server. This is required, because FSRM migration requires the drive letter to remain the same.
- Install migration tool on source server and execute it
All detailled step by step operations are here :
File and Storage Services: Prepare to Migrate
https://technet.microsoft.com/en-us/library/dn479284%28v=ws.11%29.aspx
File and Storage Services: Migrate the File and Storage Services Role
https://technet.microsoft.com/en-us/library/dn479292%28v=ws.11%29.aspx