Should make for a great NAS, but here's a few opinions from me.
To save a bit of money you could use the CPU from your current build, and if you went with Linux without a GUI (which I strongly recommend but more on this later) you wouldn't need anywhere near that much RAM.
Cooling - I originally thought no fans on an Atom server would be fine. Wrong - while still within spec, the components got uncomfortably hot
IMO. A single, quiet 120mm fan suspended in the case with some zip ties blowing over the motherboard sorted that, everything stays warm or cool to the touch now.
I was originally planning on putting the OS on a USB stick, but a few members here pointed out the drive might get worn out over time by small writes. I was thinking about doing it by going without swap, changing the logging options, etc but I finally just decided it wouldn't be a problem to put the OS on a small (4GB for me) first partition on the single HDD I'm using. Even about 6 months down the line with log files growing in size and such, usage still hasn't hit 1GB!
I don't see the point in an SSD in a file server at all
TBH, I think it would be a complete waste of money unless you used all SSDs for wanting to make it as silent as possible or something. However, you could stick a 2.5" HDD in there to put the OS on if you RAID all the space on the other drives and have to put the OS somewhere else - performance of the OS HDD really shouldn't matter much with a file server.
I agree with dirky about software RAID, it's something Linux does very well and the RAID on the motherboard will be little more than software RAID anyway.
OS - I use Debian CLI-only and can't fault it. I only really needed to attach a monitor to install the OS (from a USB drive - no CD drive needed) and some essential software but now it runs headless, only network and power cables attached. Just install the SSH server so you can log in remotely. I really wouldn't recommend a GUI for a server,
IMO it's really no easier than using CLI as there are usually options missing so you have to resort to, and know what you're doing with the CLI anyway. Also it's far more frugal with system resources, as I said before I'm using less than a gig of HDD space for the OS and according to htop, only 29MB of RAM are being used! Of course this goes up slightly under load but never comes close to the 1GB I have installed. And I don't use swap, Linux manages fine without it, especially with that much RAM spare.
Debian is pretty similar to Ubuntu when it comes to CLI, but with Debian you can log in as root by default which I like, with Ubuntu the root account is locked by default so you have to either use sudo/su all the time or mess about to get the root account working. Also Debian releases are less frequent, which is nice because upgrading a server OS to the next release could be a pain. But saying that, you could just use the Ubuntu LTS releases. Anyway, OS choice is just something that comes down to preference.
Oh I should mention with my Atom D510 server with a single low-rpm 2TB drive I manage 90MB/s+ transfer speeds, yes that's megaBYTES per second. Probably limited by PCI network card (onboard realtek is rubbish, kept dropping the connection so I bought an Intel card which is rock solid) and HDDs in server/PCs.
Hope this has been of some help.