Here is the list of components I have put together. I havn't built a Mini ITX system before and am wondering if this is a good build? Do I need to worry about any bottlenecks due to the motherboard/cpu/graphics combo? I think the build is sitting somewhere around $2400.00 USD. It is meant to be a gaming system.
You could get something far cheaper that would pretty much do the same job. i7/16GB RAM isn't really necessary for games, neither is 2400Mhz RAM. An i5 with 8GB of 1600Mhz RAM would perform so closely that you would only notice the difference in benchmarks and it would be far cheaper. Also, the non K versions can't be overclocked by the way.
Another thing, dual chip graphics card like the GTX 690 and HD 7990 are a lot hotter than the next step down ie. single chip card like the HD 7970. I'd get the HD 7970 Ghz edition, probably the best single chip card around.
I would stay away from water cooling to be honest, it isn't even much cooler than decent air cooling but it is more expensive and has the risk of leaking.
EDIT: Closed loop water coolers like the Corsair ones might be good actually, most air coolers might be too wide to fit on a mini ITX board properly.
This would be my choice:
2x4GB Crucial Ballistix Sport 1600Mhz Low Profile 1.35v C9
Sapphire Vapor-X HD 7970 Ghz Edition 3GB
Crucial M4 256GB 7mm
1TB Seagate Barracuda 7200RPM
Seasonic G Series SSR-550RM 550W
Fractal Design Node 304
Total is around $1400 and would stay way cooler and quieter and still perfectly able to play any game out there on maxed out settings.