This article discuss “how to backup and restore NTFS file system permissions as well as network share permissions?”. KB article 125996 talks about the network share piece of it, but it does not talk about NTFS permissions.
One thing that has made the NTFS permissions piece of this simpler is the Icacls tool. Icacls was developed for Windows Vista as a replacement for tools such as Cacls, Xcacls, and Xcacls.vbs. It was also included in Service Pack 2 for Windows Server 2003 and Windows Server 2008.