OK, so for now I ditched the motherboard idea. I am not willing to buy a motherboard from a fab, so later I may make a homemade board with vias, as seen here. That blog is really awesome btw, consider reading it sometime.
Well anyways I have been trying to get a 16550 UART working, so far with no luck. I have pretty much reduced the problem down to the UART or the data bus's connection to the 'expansion board' I made because I ran out of room on my first board.
I also added a nice ATX power supply controller circuit, which allows power to go to the (currently useless) IDE hard drive. It's still pretty cool though.
Well, here is the system so far:
You can see why I need to make my own smaller and more clean PSU. This 'wires going crazy shorting everywhere' business with a WAY oversized powe is beyond terrible. OK, now the computer itself: