What are you computing requirements?
I'm not sure I understand what you mean, but if you're thinking about designing and building your own fully fledged x86 motherboard, you're probably in for a lot of work...
First, which chipset do you have in mind? (Northbridge and Southbridge)
Checkout their datasheets.
Second, CPUs have a very demanding power requirements. You'd have to build a power supply capable of delivering sometimes up to 200W @ ~1V in very short bursts while keeping no more than 10mV ripple. (see
https://en.wikipedia.org/wiki/Buck_converter#Multiphase_buck) - Again check the target's CPU's datasheet.
Third, operating at high-speeds, laying out the traces of the PCB is a tedious task avoiding crosstalk and interferences.
And least - you'd have to do all that under your size constraints, which seems to be quite limiting.
These things pops to mind - there are probably hundreds of other things to take into account... This is a big one
If you can get away with building a low-end device, like those TP-Link routers, powered by a small MIPS processor, or using one of the simpler x86 compatible VIA CPUs (if they still make those...), then you would have it much easier.
Or just go with an ARM SoC. But then again, if that IS an option, you may be better just rip off a board from a portable device and installing your own firmware.