If I were going to go back and learn the ins and outs of an OS again, I'd still go back and start learning from the bootloader to the kernel and then progress from there. The kernel is the OS for all intents and purposes. It sounds more like you want to learn how to create your own Linux distribution.

Don't fret, we've all been there and done this ourselves :). Some people catch the bug and create stuff like Gentoo and Arch.