ok,heres what i got on my MV,(using same basic honda CDI)
ignore/disconnect rec/reg wires (for now)just incase??
your #2 green from box goes to the coil as earth
cant see ?,should be black out of box to kill switch,to your blk/w wire,then out of switch to earth green (frame),disconnect till sorted??
in your piccie ,is that blk/w (blk/y) going into double green,a no no?
my trigger wires blue/y into box,but y(ellow) goes to frame earth,(not coil earth)
r/blk from stator to box is alls needed to charge the C in CDI (top r/h wire)
imediately below #2 green,what colours that?,yours is 6wire box,diagram shows 5? (mines 5)
hth?,cheers mick