I have an 04 KFX 400. Battery was tore out, positive wire lead is still intact. The negative was torn off completely. I purchased a new one. The negative lead wire has a thin wire with a connector, and the other is the ground. I know where thin wire plugs in. But the ground i'm not so sure about. I have what looks like a ground wire that's currently ground to starter motor. So one end is still connected to the starter motor, the other is just hanging near the back end, what ever was connected to the end of it is gone, it's just bare wire now. Do I ground the battery to the starter motor? Tried using the manuel, it wasn't much help.

 

To sum up, is there a difference between the motor ground and the ground that comes off the negative wire lead?

 

The "Ground" on your bike is the whole chasis. Not sure details about the KFX but there should be single black wire that goes from -ve of the battery to the chasis of your bike - the metal frame. The same goes for the "ground" on the starter; it should go directly to the chasis.
To sum it up NO there is no difference between the motor ground and the ground that comes off the negative wire lead.