At risk of stating the obvious - it's very expensive. Some of the items only you can really know if you genuinely need, others are potentially based on slightly dubious logic, but it's safe to say that there is a huge scope for saving money here, or potentially re-evaluating some priorities.
If you are overclocking then obviously the 4690K is the CPU to get, but if you are genuinely focused on keeping temperatures and presumably noise levels down then it might be worth looking at other i5s as for your usage it's not going to make a vast performance difference and does come with added negative effects (noise/heat/cost etc).
The H80i is about as good a closed loop cooler as your build can manage. There's 140mm rad based options which are available to you, but if your focus is heat/noise then it's likely you'll get better results with air than you will with these types of units. A Prodigy is very flexible with regards to air coolers, even with the ODD bay populated, as long as you pick a suitable motherboard for the job. It's worth also pointing out that an air cooler in a case this compact will also effectively self-exhaust as it will line up pretty well with the rear fan mount.
The Maximus VI Impact is a slightly dubious choice right now. It's a fantastic board, effectively the best money can buy, but it's insanely expensive (double the price of some comparable units), due for replacement soon, and doesn't officially support the 4690K out of the box (you need to update the BIOS). Given your budget, it's not a ridiculous luxury, but if you aren't in a rush it might be worth waiting a month or two for it's replacement, even though its featureset is likely to be near identical.
I'd question why you need 16Gb of memory. 8Gb is likely to be enough, and if you are running memory intensive applications, then it's odd that you'd stick with the basic 1600Mhz speed when 1866 or 2133 kits are available for a similar price.
Your storage solution only you can really decide whether or not it's A) what you need and B) if it's worth the cost. As above there are viable alternatives at lower price points.
As mentioned above, a 760W PSU makes little-no sense on an ITX build. Realistically you can run your build on a 500W PSU, and you might want to stretch that into the 600-650W range if you want to find the types of high-end modular PSUs that might appeal to you, as well as giving you flexibility to add any graphics card you like somewhere down the line. On a good day you could spend a third of the price of the AX760i, but half wouldn't be a bad target either as it gives you a bunch of great options under the brands of Antec, Seasonic and XFX.
In a $2000+ gaming build it's a little odd to "only" find a GTX770 but I understand why you've ended up there. If you are running a single 1080P display (as most of us are) then spending more than this is fairly counterproductive, but I'd query your choice of card. It's very expensive for a GTX770, as you can get faster cards with better cooling solutions for significantly cheaper. There is a certain logic to self-exhausting in smaller cases, but the Prodigy isn't that small and has excellent venting around the graphics card meaning it actually has better characteristics than a lot of ATX towers. I would suggest one of these options -
If you are sure a GTX770 is all you need, get a cheaper one with a better cooling solution. You have a lot of options here but the EVGA ACX, Gigabyte Windforce, MSI Twin Frozer and Asus DirectCU II are all very popular.
If that's the kind of price you want to spend, and are happy to do so, get an R9 290. You can pick one up for around the same price with a decent cooler on it which should comfortably outperform a GTX770, and keep temps/noise under control.
If you are adamant that you want a centrifugal fan cooler, then shuffle the budget around, and try to stretch to a GTX780 with a Titan cooler (they did sell these on GTX770s but they are really hard to find at sensible prices) as it's the best reference cooler on the market and works pretty well.
As for case cooling on a Prodigy, it comes with two 120mm fans which are absolutely fine if you want low noise levels but don't move a lot of air. If you are going high end, overclocking etc, then you are probably best to ditch both and replace them with larger, higher quality options. At the back a quality 140mm is ideal, though a good 120mm will do the job. At the front you can fit a 230/200mm fan (not much different in diameter despite the name) which is good for airflow but not great for noise levels. If keeping the noise down is a big priority then I'd suggest going for a 140mm as it has a better mounting location than a 120mm. Two fans is all you need for this case to guarantee decent airflow, the vented top panel should let any excess heat find it's way out naturally.
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