TR3649 best practices for a secure configuration is a good start. And also TR3996 PCI compliance will have some info that helps secure the system. Not a DoD doc but these cover a lot of security settings.
Re: Secure configuration of NetApp product in DoD environment
Most TRs are available on http://www.netapp.com/library; no account is needed to access them. Some are restricted access and can be downloaded from fieldportal only; you need to be partner to have access to fieldportal.