You know what? You're right. The problem is, this isn't a $1,000.00 computer. It costs $1,000.00. But it's actually much cheaper as far as the component prices. Probably around 600-700 I'm guessing. I will work on researching the cross value of Motherboard --> GPU and HD --> GPU. I think they are closer to equal value/performance than you may be thinking. But I bet you're right and I need to find more of a middle ground. That being said though, a $1,000 from these places is not a $1,000.00 computer for a self build.
With what I can tell and please don't take offense if I'm wrong here. But it seems like you are very knowledgeable and good at building systems. But maybe have less experience with these websites that sell custom PC's. Give it a try, building some of these computers on these sites. This will give a really good understanding of where I'm coming from as far as price and components etc.
Here are a few of the sites I've tried.
www.ecollegepc.com/
http://www.falcon-nw.com/
http://www.originpc.com/
There are tons more, but that should be sufficient, those are just some of my favorite.
It's not that I'm not appreciative of the advice, or even disagree with it. It's just that maybe the focus is on the wrong thing, and the advice is based on a self-build rather than a custom PC website build.