What type of control box? 703 side mount or 704 to mount?
Former has wire oncolour coded bullet connectors which can be undone. Latter has two round twist lock connectors. Undo those and remove the ten pin harness that way.
If the motor has a ten pin harness connected to it, and a control box/key switch connected to the end of that harness, and it all works well, why not move everything over from one boat to the other?
The motor has been modified. It would have come from Yamaha with a ten pin connector on the main engine harness. That connector would have connected with a corresponding 10 pin connector in the ten pin wire harness.
I am not understanding the words about the electricity running backwards.
Electricity (current if you will) runs to a battery and from a battery. Not at the same time but when the battery is being charged and when the battery is powering components.
Something leads me to believe that the gizmo seen on the cam shaft for a Mercury Marine 3.5 four stroke model is related to the compression release mechanism.