For me the 'aha' moment was the microcode section of the 8-bit computer project. Just the physical understanding of how it can take a different number of clock cycles to execute an 'instruction' - and how (in this architecture) every instruction cycle has to start with the memory address switching to the current program counter, and the data from that address being loaded into a register.
I haven't gone as far as actually building a breadboard CPU, but I was able to apply what Ben teaches to build several functional microprocessors in https://www.falstad.com/circuit/circuitjs.html, starting with basically reimplementing the breadboard model he built out.. but then after watching the 6502 series, going back and being able to see and even implement some of the things that implies about the internals of a 6502 processor.
I haven't gone as far as actually building a breadboard CPU, but I was able to apply what Ben teaches to build several functional microprocessors in https://www.falstad.com/circuit/circuitjs.html, starting with basically reimplementing the breadboard model he built out.. but then after watching the 6502 series, going back and being able to see and even implement some of the things that implies about the internals of a 6502 processor.