The msi lightning requires two 8 pin pci-e connectors. A good quality psu may well have that.
But, that is an expensive card @$600.
It has a boost clock of 1176.
A less expensive top GTX680 might be the EVGA Superclocked, Signature 2 @$520.
It also has a boost clock of 1163, and only requires a 6 and an 8 pin connector.http://www.newegg.com/Product/Product.aspx?Item=N82E16814130797
If price is no object, and you want the strongest single gpu card, then look at the EVGA GTX680 classified@$660.
It is built for maximum overclocks. It needs two 8 pin connectors.http://www.newegg.com/Product/Product.aspx?Item=N82E16814130801
You should have no problem with the Noctua NH-D14. It is about the same height as any other tower cooler, 160mm.
With the two fans and towers, it will cover lots of the motherboard, so plan on using low profile ram.
As I understand it, the cm USP case comes bundled with a 550w psu that you can't use.
Is there something about the case that you really want?
I suspect that there are better options for you.