The i3-3220 can be had for $130, so you're paying $85 extra on this hypothetical. I'd save my money for some flowers.
I was thinking you might also prefer a PSU like the Seasonic G-360 to save yourself another $100, as I think the power draw of the system will be more like 150W at full burn.
Well, she tends to stick with a computer for about 4-5 years, so I thought a bit of extra computer power would be a good idea. I went with the larger power supply with the expectation that the fan would never run. Also, I really like having a modular supply to minimize the cabling. Flowers come from the flower garden in the side yard!
Is there a particular reason for RAID?
This is primarily about uptime. She's on the computer and doing stuff for several hours per day, and I would be a deer in the headlights if her machine weren't working! We've had multiple disk drive failures over the last decade, so the Raid-1 configs have paid off. (I'm assuming the SSD will be more reliable...)
Since the CPU dissipates only little heat there's no need to buy such a giantic CPU cooler as the Noctua.
Hmm, I didn't have any obvious way to choose between coolers, so picked what appeared to be a reasonably sized and high quality one. Hmm, the Mugen 3 doesn't look all that much smaller. It's 158 x 130 x 108, the Noctua is 166 x 140 x 130 (fans included -- if I take the top fan off the Noctua it's 105mm if I'm reading the spec sheet correctly.) But the Mugen is cheaper.
You could save some space by buying a mATX case.
I wanted a case with built-in sound deadening, and also plenty of room inside just in case (I had a horrible problem with an Antec case once where the SATA cables, the disk drives, and the end of the GPU card all were just a bit too close, causing the SATA cables to slowly work themselves out of their allegedly-locked socket!)
Does your wife need the dedicated GPU?
She does want to play 3D games. The Intel HD4000 is a good integrated GPU, but it cannot compare with an add-on card. She has complained a lot about the graphics performance of her current card.
Thanks for all of the responses. It definitely looks like I could have saved a few bucks had I not had to order the parts already. Next time! (My daughter will be needing a new machine in about 7 months and I might as well make it quiet too.)