Oh I see, I didn't know you got it used. From what you linked, I assume you bought it brand new. That means the build comes in at under $1000 then, that's good. You can use the same parts in the NZXT S340 you were looking at earlier, except for the white Phanteks air cooler. That is too large to fit into the S340.
Edit: You can definitely get another cooler and then maybe put a white fan on it if you wanted to keep the same aesthetic.
Here's a list of partly or wholly white 120mm fans.
Also, the S340 cannot support any disc drives. Do you still need a disc drive?
As far as I know, only high end ATX motherboards or the smaller mITX motherboards come with built in wifi. You're going with the ATX size, so it's probably easier to just get a separate wifi adaptor rather than spend too much on an expensive motherboard or get a compact motherboard that kinda defeats the purpose of going with an ATX size case in the first place.
Depends on your specific setup and what you'll be doing, but either would be a good improvement in terms of temperatures. The Cryorig H7 or a Noctua model would be better, of course. Concerning noise, you'll want a larger cooler with a larger fan, as larger fans don't have to spin as quickly to move the same amount of air as a small fan (or they can move more air for the same amount of noise and speed).
http://www.hardwaresecrets.com/cooler-master-hyper-tx3-cpu-cooler-review/6/
http://www.tweaktown.com/reviews/6958/cryorig-h7-cpu-cooler-review/index6.html