If you don't mind working with software emulation, nand2tetris takes you from logic gates up to a CPU, assembler, compiler. I'm working through the book: https://www.nand2tetris.org/book. It doesn't focus on an existing architecture like 6502 but focuses on simplicity instead to make the ideas really clear.

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!)

a good computer organization/design or intro computer architecture course will have the same effect.

the classic text is computer organization and design by patterson and hennessy.

I've got H&P on the bookshelf. It's the 'get down and dirty with a breadboard an x86 chip and maybe a soldering iron' aspect I am surfing for. 'Like Ben Eater but for x86', preferably as a course, is what I'm aiming at/curious about.

i think some logic design courses are like this. you're given a fpga dev board (that has a bunch of peripherals and ports on it) and you code up a cpu and a few memory/io controllers and then in order to do something you have to assemble some machine code and run it.

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.

Petzold's Code book is like this, without the hardware. But could certainly be combined with it.

Ben Eater has a video series called "'Hello, world' from scratch on a 6502" that you might find interesting: https://www.youtube.com/watch?v=LnzuMJLZRdU&list=PLowKtXNTBy...