...and that's just on the front end. Most of the big players contract out their PC Board construction to one of a few players and manufacture it in volume to drop the cost. Normally runs are in the hundreds of thousands of PC boards. There are only a few manufacturers that will do custom-designed small runs (100 boards or so).
Custom multi-layer PCB Motherboard Manufacturers:
Wikipedia's List of Motherboard Manufacturers:
http://en.wikipedia.org/wiki/List_of_PC_hardware_manufacturers
Sunstone (Does small runs of 100 boards)
http://www.sunstone.com/
Advanced Circuits (Does small runs)
http://www.4pcb.com/
Generic PC Board Manufacturers
http://www.everythingpcb.com/p13057.htm
There are numerous additional factors involved in doing the layout that should be taken into consideration in the Motherboard Design Process:
http://www.mbreview.com/mbr-reviews/497-motherboard-design-process.html:
Once you have the motherboard, all of the components then need to be mounted. Currently this is done on a large scale with surface mount equipment. As of 2012, Panasonic seems to be a leader in this area:
http://www.panasonicfa.com/?id=electronics%20assembly
Finally, you need to test your motherboard to see if it works right. There are so many things that can go wrong with a motherboard build that companies have evolved and developed automated testing technology, these include:
Teradyne
http://www.teradyne.com/
Hewlett-Packard In-Circuit Test (ICT) Systems
http://www.home.agilent.com/en/pc-00002%3Aatg%3Apgr/in-circuit-test-systems-3070-ict?nid=-536900137.0&cc=US&lc=eng
HP originally developed ICT to ensure the quality of the electronics they built, then started marketing ICT to other electronics manufacturers. Their most famous boardtester, the 3070, has been around for 30 years now...
The in-circuit test allows you to fire up the motherboard and test every connection simultaneously, it's quick, accurate, and cost effective for troubleshooting large manufacturing runs. If i had a choice, even with a small run of motherboards, I would much rather spend my time building a test bed, and writing a test suite for my new PCB. Then later, if I wanted to do a larger run of boards, I'd be setup to troubleshoot the entire manufacturing run. You are looking at about $250k-500k, per station, that's for a used ICT station.
I would say, if you are serious about building motherboards, you really need to join a team that does this full time already. It's been my experience that Engineers love to play, and you can get some opportunities to build your dream PCB (On your own time, of course), plus learn what you really need to know about designing and building PCB in doing so.