as stated before
the mystery black box is a speedo healer. it's plugged in line with the speed pickup. the white plugs are the stock connectors, the green ones to to the healer
the green plug with nothing plugged in by the battery is the service connector. this is normal
the PC plugs in line with the throttle body connector, it's nearly impossible to mess up. make sure the black wire with a ring terminal in the PC harness is connected to battery negative.
the white plug at the rear of the bike is the license plate light connector. it looks like you have an after market setup so they probably just used the positive from the bike and a common negative. hence the use of only a single wire
any other questions?