Many schools have OS classes that do much of what you describe. My school (CMU) taught OS in C, and we wrote a kernel, file system, and shell, and were provided with code for a boot loader.
Unfortunately, I wasn't able to find any definitive resource for this course (15-412) on the web, and it's evolved over time. But perhaps people could post links to sources and assignments for schools that do have good resources on the web.
