Any particular reason why you going with the Z97 instead of the H97? feature wise they are very similar, if you are not overclocking i would go with the Asus H97I-PLUS Motherboard
While i like Lian Li cases, and this seems very similar in appearance, i don't like the design for a GPU oriented case, seems little airflow specially with 3.5hdd. If i were to build on U2, i would use the front fan and the back fan. Haswell runs hot specially hyper threaded CPUs, given that yours isnt, still has high clocks and TDP, so dont go with a low end cpu cooler, consider at least a Scythe Kotestu
, the Asus motherboard allows for a tower heatsink to be installed due to cpu socket placement, the kotetsu is kinda slim so shouldn't have much issues, its cheap as well, and should be good enough to handle the quad you like quietly. The U2 has 175mm height clearance, so the Kotetsu should fit.
Try to get a couple case fans that can undervolt well, Scythe Gentle Typhoon AP12 or AP13 are will drop to 300rpms under fanXpert, or get Scythe Slipstream/Glidestream 800/1200rpm versions or Nexus Basic 120, all of them undervolt well and are decent for a quiet build.
I would avoid if you can a 3.5 hdd, your idea of a NAS is what i would do, get as big as you can on SSD and have your main storage elsewhere, now if you have to have some in your pc, consider a 2.5hdd, they are design for laptops where usually there is not much ventilation and they still hold very good, a scenario that you will face. Hitachi Travelstar 5K1500 1500GB
is my new favorite, but there are lots to chose from. A 2.5hdd placed on the bottom should still allow you to use a dedicated gpu, specially something like MSI/Asus GTX760 mini that come with slot blower on the back of them.
About the SSD, i wouldn't go with the cheapest you can find, try to go with a proven brand that has good support and track of their past ssds, like Samsung, Crucial or Intel. Samsung 840 EVO 500GB
and Crucial MX100 512GB
seems very good value oriented options, both offer your desired 512gb so that would be my pick. There is still another option, with the motherboard you are choosing, Asus Z97i having a bottom motherboard mounted SSD (m.2), there are very few options atm, but there are some, like Crucial CT512M550SSD4 512GB M550 M.2 Type 2280 Internal SSD
or Samsung XP941 512GB M.2 NGFF PCIe Solid state drive SSD