hi
no offence, but you are at least 5-10 years of hard work and learning away from designing your first x86 motherboard, if you ever will be able to do that. Most design engineers even the very experienced ones never do anything that challenging. One project takes almost a year from concept tull production with 8 hour/day 5day/week, plus lets say $2000-30000 funding for a project, also other engineers to be involved with it. I have designed a few X86 motherboards, thats what I do normally, but I have designed complex boards with DSPs andFPGAs before my first x86. the simplest would be lets say 1200 components and 6 layers, but 2000 components and 10 layers is more realistic.
People with skills similar to yours normally design base boards for COM modules like ETX or COM-express or PC104. The COM modules have the processor, chipset, memory and all critical circuits on it. Even this requires knowledge of computer architecture, complex and high speed digital design, signal integrity - at a high level that I think you don't have at the moment.