What do you plan to use your NAS for and how important is performance for small, medium, and large file types? How many users will access the system at any given time? How much do you want to be able to expand your system as your data grows over time (ports, PCIe slots, drives, etc)?
I would recommend you consider trying
OpenFiler which is also Linux based (rpath linux) or from the windows side you could do a basic Server 2003 install if you have access to it or are willing to put down the cash for a license.
I'm personally using OpenFiler with my home built NAS and the performance has so far proven to out-perform freeNAS in both small, medium, and large file transfers using the same hardware. The OpenFiler UI is a little bit easier to navigate once you get the hang of it and it still has a decent amount of features. If you don't care (or need) things like ZFS which isn't available in OpenFiler, you can still get away with good performance using ext3 or XFS file systems. I've had to mingle in the CLI a little bit to correct some oddities with the way it partitioned my array, but it was nothing traumatic.
I can help with what I've learned so far and I'm also comfortable with the varying Linux distributions (though I'm no self-proclaimed expert), I can give you some guidance. They also have their own user forms to discuss problems, concerns, etc.