If you float the ground from the stator, your dc powered electronics (starter, lights, etc.) can be frame grounded.
After you run your two inputs (your light circuit power from the stator and the floated ground) into the rectifier/regulator, you run the rec/reg output ground or negative to the battery and then to the frame.
You can leave the green ground wire connected to the frame, as long as you have floated the ground.
If you have not floated the light circuit ground, you cannot use the frame as ground for any electronics using the dc power. These electronics must ground back to the battery or capacitor.
The goki setup requires the frame to be used as ground as the starter is grounded to the frame. I don't have the goki installation instructions so I can't comment on how they go about handling the conversion and grounding and such.
85 Kawasaki KLT 160
85 Kawasaki KLT 110
82 ATC 70
2000 Scrambler 500