One route to understanding how CPUs work is to explore the computers that have been made in cellular automata. Golly (https://golly.sourceforge.net/) has several, including one by John von Neumann, one by Edgar Codd and another by John Devore. The advantage of course is that the physics is trivial and you can see everything that happens and step backwards and forwards.
Example:
https://timhutton.github.io/2010/03/10/30984.html
https://github.com/GollyGang/ruletablerepository/wiki/CoddsD...