You can keep the CPU and the motherboard you listed as long as you plan on upgrading your CPU to an unlocked version eventually. If not than you shouldn't get the motherboard because it would just go to waste.
That RAM you listed has a CAS latency of 11. Which isn't terrible, but why get it when you can go lower? Get this set of 2x8GB RAM at 1866MHz with a CAS latency of 9. It's fantastic RAM
http://www.newegg.com/Product/Product.aspx?Item=N82E16820233536&nm_mc=AFC-C8Junction&cm_mmc=AFC-C8Junction-_-na-_-na-_-na&cm_sp=&AID=10446076&PID=3938566&SID=
And yes you should be able to use a 4gb stick with the 8gb stick, just make sure the sets are in the right slots.
As for the SSD I still recommend going with the 250GB one, 500GB is quite a lot, and it saves money to go lower. Since you will mainly be using the 5TB of space for storage, just keep it on a large HDD as planned, use the SSD to put your OS on, and maybe a few games.
You should be able to keep the OS on the HDD if you want, just make sure that if you're using it for storage and if you're installing stuff on it that you keep it organized. Since you will still have the OS on the HDD then you will be able to boot into windows using it just like you could before.
The GTX 780 will be plenty, and saves lots of money.
If you plan to SLI than you don't need to worry about running out of space in the 300r. You just want to make sure that you have a 850W minimum PSU for the parts you will have, I will recommend one.
If you want to overclock in the future you should definitely get an aftermarket cooler. I will recommend a good deal in the build below:
PCPartPicker part list /
Price breakdown by merchant /
Benchmarks
CPU: Intel Core i5-3330 3.0GHz Quad-Core Processor ($189.99 @ Newegg)
CPU Cooler: Corsair H60 54.0 CFM Liquid CPU Cooler ($49.99 @ NCIX US)
Motherboard: MSI Z77 MPOWER ATX LGA1155 Motherboard ($189.99 @ Amazon)
Memory: Corsair Vengeance Pro 16GB (2 x 8GB) DDR3-1866 Memory ($154.99 @ Newegg)
Storage: Samsung 840 EVO 250GB 2.5" Solid State Disk ($151.95 @ Newegg)
Storage: Seagate Barracuda 2TB 3.5" 7200RPM Internal Hard Drive ($82.99 @ NCIX US)
Storage: Seagate Barracuda 2TB 3.5" 7200RPM Internal Hard Drive ($82.99 @ NCIX US)
Video Card: EVGA GeForce GTX 780 3GB Video Card ($499.99 @ Newegg)
Case: Corsair 300R ATX Mid Tower Case ($64.99 @ Micro Center)
Power Supply: Corsair 860W 80+ Platinum Certified Fully-Modular ATX Power Supply ($169.99 @ Amazon)
Optical Drive: Asus BW-12B1ST/BLK/G/AS Blu-Ray/DVD/CD Writer ($59.98 @ OutletPC)
Operating System: Microsoft Windows 7 Home Premium SP1 (OEM) (64-bit) ($89.98 @ OutletPC)
Total: $1769.82
(Prices include shipping, taxes, and discounts when available.)
(Generated by PCPartPicker 2014-04-17 01:20 EDT-0400)
First thing to upgrade is your CPU for sure. I still recommend going with LGA1150 though if you will consider selling your current CPU and doing something else. But this right here is the build you can do while still keeping your current CPU.