http://gpu.userbenchmark.com/Compare/Intel-HD-530-Desktop-Skylake-vs-AMD-Radeon-HD-5450/m33102vsm7719 That VGA is still a waste of money.
That cooler might be too big for the case, double check the dimensions
If you can, get a Seasonic G series (on sale @ Newegg, good deal for a 550W gold one) or get a corsair CXM (450, 550, w/e)
Here's what I'd do :
http://pcpartpicker.com/list/KmTMwV
If you must get a Video card, settle for nothing less than an AMD Radeon RX 460 or NVIDIA GeForce GTX 950 (GTX 1050/Ti is a better deal from NVIDIA tho)
Aftermarket CPU cooler isn't necessary. Skylake runs cool enough for stock to work under maximum load. If noise is a concern pop in something like a Cryorig C7, but H7 is probably the quietest cooler under $40 and will work beautifully. Doubt you'll need that much cooling power on an i3 though.