Perhaps also add testing costs in there. With that many components one would have to do some some or all of... flying-probe, automated optical inspection and functional testing. The testing alone would have significant setup costs in the thousands of dollars, that get small when amortized over MANY units (but I seriously doubt there will be more than a few made of these!). Given that this is an actual CPU, functional test is going to be fairly complex.
Really glad that someone has taken the time to do this project, it is effectively a work of art or an interesting discussion piece.
So basically, when I understand you correctly, a PC motherboard is only as cheap as it is due to scale advantages and lots of the parts on a motherboard being resistors etc.?
My comment about resistors was that most assembly houses will give you certain components for free because they're an insignificant fraction of the price. Also because almost every digital PCB will use e.g 0.1uF capacitors, they can buy enormous quantities. If you look at the link below you see that most of the cost is in the few specialised parts like the North/southbridge, sound card and connectors.
Here's a teardown and BOM analysis for a motherboard: http://electronics360.globalspec.com/article/3280/asus-p5kpl... . Note the BOM cost is essentially the sale price.
This is partly why Apple's stuff costs so much, because they actually price their devices reasonably (from a business sense). Everyone else works on razor thin margins to give you the illusion that hardware is cheap.
Then you have actual BOM cost which is maybe another $150-200. A 2N7002 is about $0.02 even at 100k volume. Resistors and small passives are often free, and the remaining bits are cheap.
The board is probably $100 each in small volume. Big four layer beast, not cheap.
I used www.7pcb.co.uk and Mouser/Farnell for prices.
So we're looking at a cost of up to $700-800 plus taxes and shipping. That's without any kind of profit for the designer, distributor cuts and so on. At $1k they're breaking even, $2-3k would be standard markup to cover overheads etc.