I didn't get a good answer for the GTX680 or 690 question so I will ask it again.
http://pcpartpicker.com/p/rTNhI will have ~$2.5k ready for budget. I will be gaming with only one monitor. I will be using the 2nd hard drive for Windows Backup.
Possible games that I will use:
Minecraft with maxed out graphics (and maxed GLSL shaders), expecting 60+ FPS.
Blockland with furthest render distance and max shaders, expecting 60+ FPS.
Star Ruler with max settings.
I don't care about noise, as long as it doesn't go over 80dB.