This gets brought up every time the topic shows up but https://www.nand2tetris.org is a course that abstracts how a computer works, and is worth checking out
Like, emulate gates and keep building bigger pieces until you have a function that’s a CPU. Etc.
I guess I’m thinking a bit more lower level than an emulator where you implement an opcode using normal capabilities of your language of choice.
I guess TFA is pretty close to this in ways, too.
Much faster than Logisim, UI a little clunky, but my CPU runs around 0.5Mhz and it has very nice peripherals like Telnet, graphics ram, VGA etc
Terrible name that is hard to google, but great tool.
hardcover:
https://www.lulu.com/shop/gerg%C5%91-%C3%A9rdi/retrocomputin...
or digital: