might want to go with something like: (looks up spare pc part lists) http://pcpartpicker.com/p/2ErpB
i5 4670k- great cpu.
h60 - nice and cheap water cooler that should get you 4.2ghz oc no problem, this case really wont fit any good air coolers.
asrock z87e-itx-amazing motherboard in my opinion, has everything you need for only 110$. really great and the steam machines all use it as well.
corsair vengenace 8gb- great mem kit, has nice latencys and all that. You really shouldn't cheap out ram for something like crucial ballistix sports which i regret even though i got it for 10 bucks less but with a slight performance decrease in my build. 8gb is good for a while, but if you really want 16, go for it. games will start to use it!
samsung evo 120gb ssd- great ssd and value. you don't need an ssd if you can wait a few extra seconds everytime your pc boots, and programs do open a bit faster, but in my opinion it isn't as amazing as advertised and you could spend this money on a better gpu or something.
WD black 1tb- amazing hdd and is plenty fast even on its own. got many things you would like like 7200rpm, 64mb cache, etc.
r9 280x(actually an r9 290 in disguise)- great card in my opinion, but with prices soaring, it's now 400. of course i know you wanted a r9 290, so you could think that the price is what an r9 290 will be when the price drops.
node 304- THE best mitx case ever. Period. one of the smallest that can fit the best hardware. there isnt a single case out there that can match its quietness, cooling, and stuffing hardware in it in such a small form factor. Every other case has major flaws, and ive done 17+ hours of research to confirm it.
case fans- the airflow on the stock case isn't quite great though, you would want to get these fans for even more quietness (about 20dbs with the whole thing, which was what i was aiming for) but if you dont care about noise (stock fans about 30dbs) then your fine.
tx650-still going with the "silent" road, so this psu will be plenty power, and silent most of the time. Remember, this case will get cramped when building, so modular psus WILL NOT fit with the psu right next to your gpu (unless your gpu is 170mm or less).
So, how is it? :D