I'm late to the thread but here is my opinion on your server:
If you want to have a large number of drives and have the ability to hot swap them you are best off with SnapRAID or UnRAID.
With SnapRAID you can use any OS and any file system, you can add or remove drives from the array without affecting the array. The one weakness of SnapRAID is read speed as it's limited to one drive due to the array not being a traditional RAID array but a software one. Also you can assign as many parity drives as you like.
UnRAID has the same strengths: you can add drives after the creation of the array, you can mix drives of different speeds and sizes (just like SnapRAID) and you can remove drives as you see fit. Its main weaknesses are file system: it's a non-standard file system and RAID so you will need third party software to read the drives in Windows. Also you can only assign two parity drives, which I see as an unacceptable weakness in a large array due to the inherent risks when rebuilding the array after a lost drive.
Both are really easy to use and are very flexible. I just use SnapRAID because it is simply wonderful and I intend to expand my array to 12 drives eventually, allowing me to assign three parity drives. My dream setup is a 24 drive 4U chassis with 18 data drives, 5 parity drives and on OS drive.
As long as the server is only a file server and not many people are accessing data simultaneously you won't need a hugely powerful CPU. My server has an AMD quad core 3.2Ghz with 8GB ECC RAM (usually 50% used). I use Windows 8.1 and my longest up time is 5 weeks and that's only because a power failure caused the server to crash and restart. I know this because my router also rebooted at the same time. My server is a Plex server which is accessed by 7 people.
If you are planning on running a Plex server and don't mind getting new hardware you could wait for Zen R5 and get the 6C/12T one as it will be superbly powerful for the price. Or if you want second hand you can get an AMD 1090T and a board. If you want Intel you need to look into Xeon (if you want ECC RAM which I recommend) or you can get an i7. You won't need the most powerful system as long as not that many people access the system but the more people access the system the more powerful CPU you need but if you don't intend to run Plex this is irrelevant.
For a simple file server a dual core high powered CPU will do just fine. If you intend to save power you can look into one of those Atom boards but whether it's worth it to you is another question. To me they're not worth it as they are too weak to run the server I want and they cost a lot so I prefer to get second hand hardware to save lots of money, which will take an Atom system years to earn back.
I can't help you with RAID cards but if you intend to run SnapRAID or UnRAID you need to look into a RAID card that can be set to HBA mode so that all it does is pass the drives to the OS. Alternatively you can get a PCI-E SATA card but I think an LSI 9211-8i set in HBA would be better as you can connect many more drives to it. I haven't been able to find a PCI-E SATA card with more than 8 ports so you will need two if you are planning on using more than 14 drives (8+6 on the board), which adds to the cost.
I do agree with the PSU wattage as you will need lots just in case they all spin up and they put strain on the PSU. An HD might only use 10W but if you have 10 spinning up simultaneously (RAID 5, 6 or 7) they will put heavy strain on the 5V rail. I will upgrade my 400W when I have enough drives to warrant it.