If you have not encountered it yet, I highly recommend Ben Eater's 8-bit computer series (https://eater.net/8bit/). I don't remember any other piece of material which made me grok the deep underpinnings of CPU instructions as this. There was an almost surreal moment where my brain went "ooooooh, this is how a CPU instructions is just a complex network of switches with on/off states". Ben Eater's other material is also great, he's just a good teacher.

Building on that, the "NAND2Tetris" starts, as the name suggests, with basic logic gates and packages these low level concepts Matryoshka-style into recursive boxes with the end goal of programming a Tetris clone. See https://www.nand2tetris.org/