I did a lot of research before buying anything for my "all-out" computer and got a lot of advice on here.
First off, on the SSD, the Samsung 840 Pro consistently has high ratings and you can get the 512GB version for the kind of money you're talking about. The 256GB version costs less than half that.
For the platter drive, I went with Western Digital WD2000FYYZ drives. They're the Enterprise line of hard drives and are about as fast as you're going to find and my experience has been (I've installed probably 100 in the last two years) they're pretty bullet-proof. The 2TB drives were less than $200 each.
For the motherboard, I bought the Asrock Extreme 6/ac because I wanted the built-in WiFi (which has come in really handy). The motherboard layout is great and the capacitor placement is not an issue at all.
I do want to go back to what people were talking about regarding data redundancy and backups. RAID0 has no parity, so if you lose one of those drives, you lose everything. RAID1 is mirroring, so if you lose one drive, the other is an exact duplicate so you should lose nothing.
Keep in mind that any kind of RAID solution is useless in the event of data corruption, virus infection, accidental or malicious user actions, etc. It only protects against hardware failure (as was pointed out earlier).
Go get Cobian (or something similar) and set it to automatically backup your data to external storage of some kind.
I bought the G.SKILL memory (I got the Z series and not the X, but as these guys pointed out, RAM is RAM is RAM) and it's solid and a brand that's well-trusted.
Regarding the water cooling - I bought that same case and returned it the next day because of this (also because I didn't like all the plastic parts). As far as rad placement goes, I'm not sure.