Mini-Itx Buld In Australia

I think the cpu cooler is going to be to high.

To the main part, you are pretty solid, but if you do want/need to trim things down, it's very achievable. There's also a few issues you should probably consider.

CPU cooler - Height wise, you have all the space in the world. You can fit significantly taller coolers in the Prodigy, but the issue with the motherboard you have picked is that it won't really work with that cooler. Here is an image which shows the issue. If you want to go with this motherboard, you'll need a narrower cooler (90-92mm fan based tower or a closed loop solution), but there are a number of ITX motherboards which are compatible, namely the ASRock and Asus Z87 boards.

Memory - It's tempting at ITX to go overkill on memory due to limited expansion potential, but it's worth considering if you actually need 16Gb. Conventional wisdom says that you can just about get by on 4Gb, and 8Gb gives you comfortably enough, meaning it's been more or less the standard recommend for a number of years.

Storage - I'd personally suggest avoiding the "Green" drives as they are focused on efficiency. If you ever want to run stuff from them (and it's hard to rule that out) then a Barracuda or Caviar Blue is a bit more versatile. Similarly, a 240Gb SSD is great, but to a degree it's a luxury. Most people are unlikely to need that much high performance storage, so it's certainly an area you can cut back, especially if you have a secondary drive you can run occasional programs from.

Graphics - Nothing wrong with a GTX780, but there's a couple of things here. Firstly, a super compact case often benefits from an exhaust-blower reference cooler, but the Prodigy is much more flexible in that regard (it has better graphics ventilation than most towers with the stock side panel) so you can more or less pick any cooler you like. Also, the model you chose is quite expensive without really providing much benefit. A similarly specced Gigabyte Windforce is $100 cheaper and if anything will perform better. Secondly, a GTX780 is arguably overkill for a single 1080P display. Given how well modern entry level cards handle this resolution now, your performance/dollar return is always going to be pretty poor, as it's right at the top end of what is sensible. You can make a serious case for spending (a lot) less on a GTX760/GTX770, even if it reduces the potential lifespan

Case - I'm a big Prodigy fan, but I also concede it's got some issues. As a truly portable case, it's not great. It's very big for ITX, wider than most ATX towers, quite wobbly even when ballasted with a chunky PSU and the handles aren't nearly as helpful as you might think. Something in the Coolermaster Elite 130, Fractal Design Node 304 or even the EVGA Hadron Air area offer much more practicality with regards to how easy they are to pick up and move around, all with varying levels of ability to fit stuff in. If you want compact performance, I'd definitely suggest the Node as you can fit a Hyper 212 in there (with a suitable motherboard), the main downside is a lack of optical drive support. If you do go with a Prodigy, then it does give you a really flexible platform - it'll take more or less any CPU cooler, any reasonable number of storage devices, no specific need for modular PSUs (unlike the super compact cases where space is a big concern). Upgrading at the very least the front fan is definitely advisable as the stock fan sits too low in the case to really do an awful lot, going to a larger size (140/200/230) positions it more centrally.
Also, avoid the windowed version(s), they remove all the venting for graphics which can have a pretty nasty impact on your temperatures.


Places to save money
There's no reason you can't knock $400+ off this build if you had to, it wouldn't have a significant performance effect.
Go non-OC i5 and H87 board (or even cheaper) - this saves a load of money and given most games are predominantly graphics-bound, it won't make a huge difference in-game. Also removes the need for a CPU cooler.
8Gb of ram is likely to be sufficient. If you go with anything other than Z87, you can drop to DDR3-1600 which might save a little.
Half the SSD size if you can. This is totally down to how you use your PC, but most people tend not to have their entire games library installed at one time, and even then games run fine enough from HDDs, it just speeds up loading times etc.
Save money on graphics if possible. As I said before you can pick up GTX780s from $100+ less, and looking at cheaper models will potentially net you massive savings. As a point of reference I use a GTX660 and there is literally nothing it can't run at fairly respectable settings at 1080P. If you are desperate to run high levels of MSAA (and other demanding effects) then you do need to spend more for particularly demanding games, but often the differences are barely noticeable.
Potentially change the PSU and ditch the cabling kit. Prodigys have a fair amount of space for cable tucking, and a 500-600W PSU only has so many cables. Additionally, due to the PSU "box", modular PSUs can be more trouble than they are worth here, there isn't a terribly compelling argument to use one. I use an XFX Core 550 in mine, and had no major issues.