Run stand wiring
Fuses are always good on wiring that is designed to be connected / disconnected.
Dont over complicate things.
You must have a dedicated ground to tie everything together.
BTW, they are 3 separate systems only tied together by the ignition switch.
Ignition...
EDIT: the MP diagram is flawed. the ballast bypass should come from IGN 2 NOT the yellow ST (Start) wire
Charging...
EDIT this is good for charging but they over simplified the ignition in the drawing
Starting...
EDIT: @mattox in a different thread reminded me that there is a separate ST (Start) terminal on the ignition switch and is used to activate the starter relay