IAmBecomeLinus

Go with the Xeon build it will last you much longer and has more room for expansion. The life of that system might be another 10 years as a file server with hard drive and networking upgrades over time.

Just swapped it out to a single 8GB 1600mhz ECC so I can upgrade to 16gb in the future (although I doubt I'll ever need to for what I'll be using this build for).

Is there any reason why you chose Ivy Bridge in the first list? Why not Haswell?
 
Both lists look pretty good to me though.
 
Just make sure you run fans over those HGST NAS drives. They run on the hotter side of drives.

Intel has just unveiled Thunderbolt 3. It will supposedly utilize a Type-C connector to support a 40 Gbps connection, thats 2x the speed of Thunderbolt 2 and about 4x the Speed of USB 3.1 by sacrificing it's display-port capabilities.
 
"With a total bandwidth of 40Gbps, Thunderbolt 3 offers a tantalising glimpse of "one cable to rule them all." In theory, you could use Thunderbolt almost everywhere: to power your laptop, to power and drive your 4K monitor, and to power and connect all of your external peripherals. The one obvious exception is external graphics cards, with all but the lowest-end GPUs still drawing more than 100W. By supporting USB 3.1 and jumping on the Type-C connector, Thunderbolt 3 may actually be the interconnect to usher in that tidy-cable utopia."
 

 
Original Link:
http://arstechnica.co.uk/gadgets/2015/06/thunderbolt-3-embraces-usb-type-c-connector-doubles-bandwidth-to-40gbps/

Everything is so ugly

Intel has just unveiled Thunderbolt 3. It will supposedly utilize a Type-C connector to support a 40 Gbps connection, thats 2x the speed of Thunderbolt 2 and about 4x the Speed of USB 3.1 by sacrificing it's display-port capabilities.
 
"With a total bandwidth of 40Gbps, Thunderbolt 3 offers a tantalising glimpse of "one cable to rule them all." In theory, you could use Thunderbolt almost everywhere: to power your laptop, to power and drive your 4K monitor, and to power and connect all of your external peripherals. The one obvious exception is external graphics cards, with all but the lowest-end GPUs still drawing more than 100W. By supporting USB 3.1 and jumping on the Type-C connector, Thunderbolt 3 may actually be the interconnect to usher in that tidy-cable utopia."
 

 
Original Link:
http://arstechnica.co.uk/gadgets/2015/06/thunderbolt-3-embraces-usb-type-c-connector-doubles-bandwidth-to-40gbps/

You know what's annoying, people are saying that they're taking Apple design and merging it with the functionality of USB.
 
Intel designed both USB and Thunderbolt. Apple was probably asked by Intel to help bring this product they made to market. Because of this, they will most likely be cross-compatible with each other and I can't wait to get this as a standard. Apple new what they were doing with the new MacBook!

Firstly, thank you for your input! I really do appreciate it, After stressing over it, I've decided to just let my GPU run on air and put my CPU under an AIO (The Cooler Master Nepton 240m). When I'm doing my upgrades next year I'll put in a Custom Loop (hopefully I'll find a way to keep atleast 1 3.5" bay by that time). As far as the Prodigy m, It's actually harder to fit rads and such in there. Even though It's alittle larger than the original prodigy, It's space is taken up by allowing a Micro-ATX system to be installed, losing some of the compatibility with Rads and such. Again, thank you for all of your input.

Haven't laughed that hard in a while.

big deal, OCZ mastered self destructing drives years ago.

^ What he said, other than the motherboard choice. Each header can support 2 ports each so you are good to go. Also, why not just paint the stock 140mm fan? 
 
One minor thing is that PCS cooler is thick- so I can't guarantee it will fit in completely.
 
I can't recommend the z97N-wifi at this stage, the BIOS is extremely frustrating and needs a lot of work. I am trying my best to work around it but there is still a 50% chance that Windows will hang during boot even if you OC a 100 MHz more on something like the Pentium G3258.

NZXT 1U01? I have one for similar reasons.

I understand the logic of SP fans for the front grill as I recently made a similar decision with my Fractal Define Mini. Although the front grill looks restrictive, it's still not really lacking enough space to need SP fans. Well, in my case, I bought one SP and one AF series Corsair fan for the front grill. I decided AF was sufficient for the intakes, however because of the position of the front HDD cages, it was extremely limiting in the lower fan mounting position, so I bought an SP fan for that slot. 
 
I guess what I'm trying to say is - AF is fine, even with the little intakes, unless it's also blocked by other things, such as HDD cages, cables etc. One of each worked for me perfectly.

Wow @.@ I run to the bathroom and when I come back there's an explosion of posts.

Yeah, I bought an Asus ROG g750jz. The first time I saw it on the WAN show, i fell in love with the look, then Linus and Slick did a short spot on it once (I don't remember which WAN it was on) but I decided to pick one up for School. I totally love it.