I traced the wires from the pickups (center and outer). The center wires were yellow, and the were joined together with a wire connector and red wire was output. The outer rail wire was black. I found the molex like your pic. Now a final, and embarrassingly basic question. I expose some of the red and black wire before the molex, and then solder one end of the diode to the exposed red wire, and the other end to the exposed black wire, right? I couldn't discern that detail for sure from your pic. I have shrink tubing as you suggested.
I don't want to make any assumptions on a brand new engine. I am a quick learner, so I won't be asking this again!