IWTL: How to make my own computer from scratch

I mean starting at a very low level with Eagle; I don't mean building a gaming rig.

I read about the Qi Hardware Ben NanoNote and that it is seemingly partially open source. Same thing about the Raspberry Pi machine, although I don't know if it's open sourced.

I've taken digital electronics in the past and know a little bit of basic DC circuitry. I also work on kernel code at work (bug fixing mostly). I just don't know how to put it together and create a system with what I know.