If i am getting this right, this build would cost $1087 on iBuypower (don't know if this includes shipping). A similar system in parts would only cost about $50-100 less (including shipping). So the value you get is pretty decent, meaning it is not a rip-off.
The NZXT Guardian is not a very good case. Besides the looks (which is personal opinion), the cable management is awful and the airflow doesn't look too good. I know, it will come pre-assembled so you don't have to hassle with cables, but bad cable management also means worse airflow. Sadly the selection of cases at iBuypower is not that good. The only one in the same price range i would suggest would be the Coolermaster HAF 922.
An absolute and total waste. The motherboard already has a build-in LAN port which will work equally well.
This is really a personal thing, but i don't like Gigabyte boards. My suggestion would be either Asus P8Z77-V LX or Asrock Z77 extreme4.
(again, this is just personal taste, Gigabyte is a good manufacturer)
Why do something simple, when there is a complicated way?
Only thing I would change would be your main HDD. I would use the 1TB as a backup/storage drive and an SSD(at least 120GB) as the main HDD. It's a world of difference in boot up times and program execution times.