If you're paying that much for a system, it'd be a ridiculous waste of money not to overclock, the cooler is a waste of money otherwise. And I'm personally not a fan of the R9s - they're massive power hogs and require huge cases to run, I would get a GTX 780TI instead. You also definitely want to get a mass storage drive - even 256GB won't get you very far these days. You also don't need Windows 7 Ultimate either - get Pro or Home Premium, that will save a lot of money.
Do something like this:PCPartPicker part list
/ Price breakdown by merchantCPU: Intel Core i5-4690K 3.5GHz Quad-Core Processor
($239.99 @ Amazon) CPU Cooler: Thermaltake Water 3.0 Extreme 99.0 CFM Liquid CPU Cooler
($104.99 @ Amazon) Motherboard: ASRock Z97 EXTREME6 ATX LGA1150 Motherboard
($161.13 @ Newegg) Memory: G.Skill Ripjaws X Series 8GB (2 x 4GB) DDR3-2133 Memory
($79.99 @ Newegg) Storage: Crucial M550 256GB 2.5" Solid State Drive
($146.99 @ SuperBiiz) Storage: Seagate Barracuda 1TB 3.5" 7200RPM Internal Hard Drive
($52.92 @ Amazon) Video Card: Gigabyte GeForce GTX 780 Ti 3GB WINDFORCE Video Card
($649.99 @ Newegg) Case: Fractal Design Define R4 Blackout with Window ATX Mid Tower Case
($89.99 @ NCIX US) Power Supply: EVGA 850W 80+ Gold Certified Fully-Modular ATX Power Supply
($109.99 @ NCIX US) Optical Drive: Lite-On iHAS124-04 DVD/CD Writer
($23.99 @ Amazon) Operating System: Microsoft Windows 8.1 - 64-bit (OEM) (64-bit)
($94.99 @ Best Buy) Total:
$1754.96Prices include shipping, taxes, and discounts when available
Then add a second GTX 780TI later on.