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About writing your own OS - it is easy to do a "pseudocode write" as it were, of an operating system, without having much idea of what the actual machine (CPU, memory, bus, disks, and other peripherals) behaves. I've done it myself. I have a book called "The Design of Operating Systems for Small Computer Systems" by Stephen H. Kaisler, which does precisely that.
To understand what the machine is actually doing, you have to read books like "Computer Architecture: A Quantitive Approach" by Hennesy and Patterson, "The Intel Microprocessors" by Brey, etc. It's a lot of hard work, but that's part of the fun. And all worth it in the end.