Ok, there are a couple of things, are you running ONTAP 8.0 or higher?
We have been running the CNAs since November of last year when our newest 3160 cluster came online. There is nothing to configure on the filer side for FC connectivity. Obviously there is all the standard Ethernet configuration for IP based traffic.
Your VSAN does have to be configured and up and running. We are using Nexus 5010 and 5020 switches. I only know the basics of how those are configured, our network guys have taken over the connectivity now. I had to do nothing other than provide them the WWPNs on the filer side.
Link UP, but link not connected would lead to me double check the zoning and VSAN configurations. Until the network guys completed our setup, we saw the same thing.
If you haven't read through it yet, TR-3800 (http://www.netapp.com/us/library/technical-reports/tr-3800.html) gives step-by-step instructions on configuring an FCoE environment with Cisco Nexus 5000 switches. Please note that on the 5548 / 5596 switches class-fcoe must be created, where on the 5010 / 5020 switches it was there by default. This is covered in the latest version of the TR (version 2.0).