XL20014

I'd leave the SSD as it is and swap out that Corsair water cooler with a Cooler Master Hyper212 EVO, which cools just as well unless you're into some ludicrous overclocking, plus it's about $30 cheaper. I have one with my Ivy Bridge i5-3570k @ 4.2 GHz. While you're at it, add an extra 4 GB of RAM to the build.
 
As for buying WIndows....that's up to you, if you catch my drift. 

Customs aren't always cheap. Last I built one I had to shell out extra bucks to get my hands on a specific manufacturer's hardware which Dell or HP's pre-builts did not have in them.
 
Anyways, its always good to custom-build what you want. That way you can build a PC cost-effectively and choose ONLY the stuff you want without having too much scrap junk under the hood. For example, if you want say 12 GB RAM and a GTX780 for yourself, you won't end up with a pre-built which forces you to have an ultra-advanced SSD with your desired setup which has absolutely no use for you and instead adds to the budget.

As long as the person who bought the rig is happy with what they got, then it's not my place to start an argument just to tell them they're wrong. He seems pleased as punch, so it is what it is.