Parts all cleaned up.
Now time to check the stator and flywheel magnets. I did test the charging system before I took it apart and it was producing voltage just fine. I also know that when these Kohler Command engines get hot the double sided tape that holds the magnets gets brittle and the magnets fall off.
As I suspected, 2 magnets had let go of the flywheel and were now stuck to the stator. The system will produce voltage with only 4 magnets, but just not the full 16 amps this system is supposed to produce.