Prepared to by CPUs by the 1000 tray? How about buying graphics cards a few hundred at a time? Thats the only way you are going to get better than retail prices on them, all parts will be branded and its best that way, as that protects your investment as you get to keep the warranty on the parts. I would stick with standard motherboards for a while because you wont be able to commission ASUS or MSI to make you a custom one, but that also leaves the issue of unlocked BIOS which can lead to more issues than a locked one if people decide to play around in it.
Anyway, unless you have a lot of capital you will need to begin as a computer assembly from retail parts deal, you arent going to be able to come anywhere near competing with HP, Dell and the like on prices unless you have quite a bit of capital to venture on the start up.