A few observations and/or questions...
Why have you settled on 10 drives? A pro license bumps you from 7 to 20+ drives so you're not really utilizing it if you upgrade. If you're trying to reach an eventual size for your array, could you not achieve the same result from just using larger drives in a smaller array? I would attempt to maximize a "plus" license (a 7-drive array) if it were me. After a cache drive, though, that actually becomes 8 drives. That will sve you a few bucks on the pro license.
The Lian Li PC-Q25B is a very popular choice for such a "plus" license setup. However, the Bitfenix Phenom has just been made available for pre-order. The mini-ITX variant can support 7 drives. Not sure about 8. Either way, it's cheaper than the PC-Q25B if you're budget-conscious. Both cases are more appropriate for a file server, and a 5-in-3 cage will end up costing you a lot of money when you finally have to go down that road with the case that you picked. the caveat on both of these cases is that they'll require a mini-ITX board. most haswell mini-ITX boards I know of have just 4 SATA ports, but you can always add a cheap expansion card down the road. It'll help offset some up-front cost.
Is money the only reason you're not bumping up to an i3 processor? Otherwise, the speed bump coupled with hyperthreading would give a significant performance increase. It might be overkill if you're transcoding, but a little money to make something a bit more future-proof can help.
I don't think your cache drive needs to be that large. You could probably get away with 250GB, but the smallest Scorpio I saw was 500GB so that might be the thing to do. it's not a huge savings, but it's betetr than nothing.
I wouldn't spend money on an aftermarket cooler for such an underpowered processor. Just use the one that comes with the processor. it's all you'll ever need. Heck, if you save them oney on the cooler, you can pretty much afford the entry-level i3. It's a much more worthwhile upgrade.