Opinion on universal wiring harness

As it sits currently this is how it looks. I know the rest of the msd6al unit is correctly installed but I was unsure if the switched + 12v should still be wired in with the alt and regualtor View attachment 1715907174
Yes that is a correct way to connect it. The on/off wire will be on with key in Start as well as Run. it doesn't matter if the ballast resistor is there or not.
The voltage regulator reads the system voltage on Wire J2B. When the voltage is lower than set point it closes a connection between R3 and ground. A little more here.