Take a microprocessor class where you build a 8088/6800 board and program it in assembler. Then there is no more magic behind the computer and it becomes a pretty strait forward machine.
If you'd like to work with real hardware, +1 to the Ben Eater suggestion. He sells kits for all the components for an 6502 machine so you don't get bogged down in sourcing them. Great videos too.
(Quick edit, not 8086, showing my inexperience with hardware!)
the classic text is computer organization and design by patterson and hennessy.
my understanding is that it is a substantial undertaking, especially if you're interfacing with hardware peripherals.
alternatively you could write a mips (subset) emulator and assembler in python and probably get the same understanding in a fraction of the time.