I just put in a second battery, replaced fuses in front, new voltage regulator, and checked all wires. I have the Kokusan system. Could the stator be going bad?

 

Check the resistance between the yellow wires leading from the stator to the regulator. Should be some resistance between each other with no yellows shorting to ground.Since it's a 2002 the manual wouldn't correctly show other tests but the 2004 manual should as that's the year the ignition has been upgraded to. 2004 Polaris Sportsman 700 Service Manual PDF Download