Ouch, that was painful to read. First off, I suggest using Newegg for all of your computer purchases if you live in the US. Very easy site to use, and usually much better prices.
If you get the 560, then get the TI version, it is significantly faster and worth the money.
You don't exactly need the i7. If you want, I'd go as far to say as get the 3570k instead.
The PSU that comes in the Sonata is not up to snuff to power up the 560 and a 2500k/3570k. I would get a Corsair PSU at least at 600w. On that note, the difference between a full tower and mid tower is how big it is. Full towers usually have a ton of 5.25 slots for optical drives.
Newegg.com - CORSAIR Enthusiast Series TX650 V2 650W ATX12V v2.31/ EPS12V v2.92 80 PLUS BRONZE Certified Active PFC High Performance Power Supply
Do you plan on watching BD movies on your computer? If not, then no reason to have that drive.
I would get this RAM instead. Terrible experience with Crucial back in the DDR2 days.
Newegg.com - CORSAIR Vengeance 8GB (2 x 4GB) 240-Pin DDR3 SDRAM DDR3 1600 (PC3 12800) Low Profile Desktop Memory Model CML8GX3M2A1600C9
You don't need a sound card at all unless you will be running 7.1 right off it. Then again, most onboard audio has an optical port and support for 7.1. You can save a bit of money by just taking that off your list. Long as you get a quality board then onboard sound will be fine.
Since you like Asus motherboards, you would be fine with this.
Newegg.com - ASUS P8Z77-V LE PLUS LGA 1155 Intel Z77 HDMI SATA 6Gb/s USB 3.0 ATX Intel Motherboard
Since you have an SSD in your MBP then I would suggest picking one up to compliment that 2TB drive with your OS and smaller programs. It really makes a difference.
You can get something like a Vertex 4 or Crucial M4.
Building a computer is really easy as everything is pretty plug and play, and connectors only go where they are intended. If you have to force something, it probably doesn't go there.