>won't you just pick up the Intel reference manual and flick through it?

The Intel reference manual is incredibly bloated and dry reading. Yeah, it has literally everything you would want to know. But good luck trying to understand all of it in a reasonable amount of time.

I learned x86 while studying buffer overflows in college. We used Hacking: The Art of Exploitation which walked us through most of the core concepts really well.

https://www.amazon.com/Hacking-Art-Exploitation-Jon-Erickson...