Righto then.
You say this is for mainly Minecraft and Gmod. Firstly you need look at how these perform.
Minecraft is inherently a single threaded with Bukkit allowing for plugins to offload to other cores. But rarely will it use more than 2 cores, unless you custom code the plugins to do so. Minecraft on the server side (especially when lots of players and/or lots of mods are involved) loves RAM. Like Tons of the stuff!
Gmod is very similar in respect to minecraft, however as the client has a copy of the map, it doesn't actually need to serve it like minecraft does. Thus it has a far far far lower RAM usage.
As both these games are not threaded/lightly threaded, they favour fast processors over number of cores.
So, the AMD opteron 4334 is not ideally (if at all) suited do this. It has a high clock speed, however its single threaded performance does not match this and its actually a very poor processor unless you are running applications that favour cores over clock. Plus IMO the C32 Socket is pretty dated.
So your current budget for processors stands at $380. So instead look at a Xeon E3-1246 V3. Its just an i7 4770k but cheaper at only $280. Why the xeon over the i7? Well ECC RAM support. In single threaded performance, it has almost double the throughput of the Opteron.
For the motherboard (sticking with ASUS and a server grade Mobo) there is the P9D-M Which is a M-ATX form factor. Like the AMD board, still has ECC support and the IPMI. Plus the other bells and whistles. Which is $218.
However, I'd go with the P9D-C/4L. Just like the other board, except it is an ATX form factor and has 4 Gigabit LAN. (TBH this wont matter much to you) But the main reason I point this board out is because it is currently cheaper at $185???
AS A NOTE
These components are on the LGA 1150 platform so unfortunately it is limited to both UDIMM with ECC and only 32GB. But I will also say, you would never use 64GB of RAM on a single minecraft server.
TBH you won't really pass 16GB (unless you are running Wynncraft).
So to save money (and cater to the limitations) Corsair Vengance Pro will be just fine. $349.
As for the case. Get something from Fractal. Like the Define R4 $99 (in sale at the moment)
If you want to stick with a Noctua cooler. NH-D14 is nice. $78 (sale) However tbh, a Cooler Master Hyper 212 Evo will do the trick just fine at only $34 (after rebate)
PLUS why on earth are you going with a referb drive???
Anyway, after chucking that through the lumber mill and seeing how it contorts. The Final price (using the less expensive Mobo and noctua cooler) is $1094.99
Much cheaper and still perfectly overkill for your needs.
Remember that a server isn't always about the class of components, but rather its task; and if the parts fit the task then nothing is wrong.