Is there a ground to the frame? Stock is bolted to metal battery box - see pic.
Basic wiring harness $25 - see pic.
When I had a problem with my wiring harness before I unwrapped my harness to search for a loose wire. I bought the basic wiring harness and plugged it in on my bike to see if my electrical parts were OK. The basic wiring harness starts the bike without the ignition switch, kill switch and no battery or accessories. Once I knew all my electrical parts were OK and the bike would run. I removed my bad wiring harness from the bike, unwrapped it and started looking for the short in my harness. I found it it was a loose ground wire in the harness.
www.whizzercruzzerparts.com Paul has the basic wiring harness, but your gonna need the 6 pin AC CDI as the basic wiring harness CDI plug is for the 6 pin . Also ask Paul if you need an adapter plug to plug the basic harness in to your 6 coil stator NE-5
I'm suggesting the basic wiring harness to help you speed up trouble shooting and eliminate the obvious.
To turn off the motor using the basic harness just hold open the compression release lever
A Tip: If you decide to remove the harness from your bike. Tag all the wires with a number and letter system.
I know the all wires are color coated but things become real confusing real fast once it's all unplugged. This way by numbering or lettering all wires there is no question what goes where.
If you were thinking of buying a new wiring harness. The NE-5 wiring harness is not available any more.
I don't think the Cruzzer wiring harness plugs match the accessories plugs on the NE-5.