I would personally get a new hard drive...the reconditioned drive was sent back for a reason, though sometimes it could be because it came from another PC that was parted out, but you wouldn't be able to know that.
As far as an OS: Windows if you game, or use specific Windows programs, otherwise, install Ubuntu. (that's my rule of thumb). I'm waiting for Ubuntu and Linux in general to get better at supporting the use of Windows executables, though there's still a long way to go. This looks like a gaming machine though, so get Windows (the OEM, not retail)
Active PFC psu's in my experience are built better than non-PFC ones...so you have a pretty sweet PSU picked out.
Everything is looking good...you can skimp on the optical drive
because they're pretty much the same, just with different brand names imho. And, I'd ditch the stock cooler if the cpu comes with one if you plan on oc'ing it. The Cooler Master Hyper n250 is a solid performer from what I've heard.