It turns out my original selections aren't much different in total price than yours. I may not remember the total correctly, but with the 3TB harddrive it's not much different at all. My original tower was double the price, and mobo might have been expensive (not available from newegg now and I don't remember what it was), but the 1000w PSU is not much more expensive, and 16 vs 4 gigs ram is a $150 difference.
Right now the prices are virtually the same, roughly $100 difference between them, without mobo but including 3TB harddrive. Yours is obviously the better choice because of the sapphire 6950, but it has low ram. Add mobo and it's between $1300 - $1400. Add full Windows 7 instead of OEM and it's about $1500 which is not far off my original choices. The difference is a more expensive and better GPU instead of more expensive and better ram and tower, which just makes sense. The difference in PSU is negligible.
"Better RAM" isn't really accurate, since that implies that you will see some tangible performance increase from the RAM. Unless you are editing images that are 15,000x15,000 pixels, or rendering video, anything more than 4GB is just wasted money.
As for OEM vs full Windows, the only real difference is that the OEM version is tied to whatever computer you install it on first. You can upgrade without causing problems, unless you change your motherboard, in which case it will detect that it is a "new computer", though often you can choose to activate by phone and explain that it was an upgrade, and even with a motherboard upgrade, the support person who you got might let you activate.
As for getting a 3TB HDD, my advice would be don't. 2TB HDDs are already unreliable enough, adding another TB, more platters, more drive heads, all in the same size space is just asking for drive failure. If you have money to spend, I would start out with a good 1TB HDD and a 128GB SSD. The performance gains of an SSD are extremely noticeable, and 1TB HDDs give good speed without the failure problems of higher capacity drives. Storage is easily expandable, so unless you need 3TB right now, there's no need to buy more. The CM 690 II has 6 drive bays, 7 if you count the hot-swap bay on the top, so you really don't need high capacity in a single drive.