Go with the LSI MegaRAID 9261-8i and add the optional BBU (Battery Backup Unit) to prevent data-loss in case of power outage.
As money seems not to be your biggest concern, don't use the WD Blacks! WD Reds are fine, but as far as i know WD only recommends them for up to 5 drives. Go for the 4TB WD Raid Edition drives - or Seagate Constellation or HGST Ultrastar. Those drives are a much better fit for the LSI-Controller. Their firmware ist optimized to run in an Raid-Array. The WD Black is optimized for single use. Keep in mind, that the more drives you use, the more drives can fail. So use Raid6 in spite of Raid5 which leaves you with 24TB usable disk-space. If you go with an 12-port-Controller and add an additonal boot-drive, you could use that in Raid1. Or use the (Fake-)Raid-Option on the Motherboard.
I personally would use a different case. But i'm excited to see, what you are going for and how you are modding the case to house all the hard drives. That said, you probably don't have the space to use a bigger board! But i'd much recommend that. Either you want to add a second RAID-Controller, an external Storage-Subsystem for backups or an additional network card (more ports or simply 10GB/s) some day. Therefore i would go with a "real" server-board from Supermicro or Asus. Along with that: ditch the i3 for a small Xeon-CPU! B)
Personally i find that unnecessary for a server! You boot your server up along with your daemons and everything sits in the RAM and runs from there. No need for an SSD for a couple of reboots a year. On the other side: you definetly want an SSD if you are planning on using a database-service (with huge tables).
I myself would much prefer seeing a Linux-based operating system running this machine! ;)
Sorry, a lot of rambling from me, but i often think about how my personal ideal home-server would look like! ^_^
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