1) Agree with ryguybuddy. Actually, you can probably max out your CPU with a much cheaper ($25) Hyper212 or Cryorig H7, so spending $150 on a cooler is rather silly. With these savings you could move up to an i7, should you wish.
2) Agree with ryguybuddy. Also, 650w is a lot more than you need, you're probably fine and then some with a 450-500w unit.
3) Again agree with ryguybuddy. Also, you might want to go with an M.2 drive, not because they're faster, but they draw less power and would get rid of a lot of wire mess in your case.
Another thought: That motherboard is ridiculously expensive for socket 1151, why that choice?