CPU:
i5-4670k YEP! i7 if you can afford it as hyper-threading is going to see more and more action now that AMD is using a
similar sort of architecture and game consoles are moving towards high core count approaches.
Motherboard:
The MSI Z87I and ASRock Z87E-ITX would be my shortlist if I were doing an 1150 socket ITX rig right now. I think you are on the right track here picking out a board with heatsunk VRMs and wifi/BT.
I like the ASRock better for a prodigy/phenom build because it makes better use of available space on the board, with 6 SATA ports and the CPU socket positioned further from the PCIE slot, which believe me, is a BIG deal come time to start tinkering with overclocking and picking out an HSF. I am currently working through my limited HSF options on an ITX board with a less ideal CPU socket placement. The Bitfenix ITX cases have the horizontal and vertical room to accomodate a lot of HSF options, but only if the board plays nice. These cases also have a lot of drive bays, which will always go underutilized on a board with only 4 SATA ports. If you decide on a more compact ITX case (which is what I wish I had done differently with a recent ITX build), The MSI board makes more sense with the lower price point and many of the nicer low profile HSFs will fit such a socket position alright so it's OK.
GPU:
Long GPU's in this case may require removing the top drive cages, making the phenom case a huge heap of underutilized space. I like AMD right now over Nvidia because of openCL trending, which favors their cards. Otherwise go with your preference if that doesn't matter. There's almost always a "best card for the money" in every price class but that's almost day-to-day trending so it depends on when you buy. GTX760 is a good card if you can take it for the right price.
RAM:
If you have the opportunity to get a low profile kit, take it, otherwise, stick to kits with heat spreads that are no taller than the PCB.
PSU:
If the phenom case is internally the same as the prodigy, which I expect it is, that RM550 won't even fit in there. Maximum PSU length that fits comfortably is 140mm. I went with an FSP 400W Aurum S Gold+ unit for my Prodigy build. Fits nicely and is a great looking unit.
CASE:
I just did a build in a Prodigy, which I believe is the same case internally as the phenom, if not, maybe some of the below will not apply, but I am sorely disappointed with mine.
- For an ITX Case it is HUGE, same size as many mATX cases and very WIDE. Upon initial impressions, this seems like it will be an alright tradeoff since the case has so much potential. Unfortunately, on closer inspection one realizes that most of the potential in this case is in the form of the word "OR." In almost ANY configuration there is a lot of wasted space in this case. I believe there are other ITX cases out there that are better suited to the ITX concept, and actually compress the machine size down enough to make the ITX tradeoff viable.
- Very poor cable management. (it's mostly just a tuck-n-stuff operation down around the PSU area, and you can tie stuff up to the HD cages I suppose.
- Side-panel USB/Audio/Power/LED means those cables can not be tucked/managed very well (because those cables must remain loose for access to that panel).
- Side-Position of USB/Audio/Power/LED is not as convenient as I would have thought. This actually limits placement of the tower in lots of furniture to less than ideal place (out in the open). This is a hard case to tuck away in a "slot" or "tower" hole in a desk or media center without loosing control over the machine.
- Front panel 120mm fan mounts. There are 2. Only 1 can be used while an optical drive is installed. The sad thing- if they had moved the holes down just a few mm, it would fit (2x120mm does fit below the drive, they just didn't put the holes in the right place, -design oversight-).
- Top Panel 120mm fan mounts are not usable with an optical drive installed. But 1 of them would have been, if they had moved the holes back just 5mm or so. -design oversight-
- The Audio jacks are the lowest quality I have encountered in any consumer audio device to date. Lowest bidder parts here for sure.
- Side panels are nice and heavy, but don't install with much grace or precision. The thinner panels on $40 cases I have used in builds all had a tighter fit/finish with the "frame."
- The HD sleds are garbage, worse than any $40-case sleds I have used. I've done builds in cheap NZXT and Rosewill cases, and they had much better quality sleds.
- The plastic "handles" on the prodigy (not applicable to the phenom case), do not inspire confidence at all. I'm scared they will break every time I move the machine.
- The only other builds I have done in similarly priced cases have been with CoolerMaster brand cases, like the Storm Scout. Dollar for dollar the CM cases delivered a lot more precision, quality, strength, and attention to design details.
- I would not buy another Bitfenix case, unless they cut their prices in HALF.