have to pull ground to kill it or use kill switch.
The kill switch stops the bike? Did you mention this before?
If the kill switch kills the engine, it narrows things down quite a bit.
The red wire from the battery is connected in the ignition to the black wire that feeds the kill switch.
That black wire also feed the cooling fan, the regulator/rectifier and the fuse box.
It isn't a fused wire, it provides power to the fuse box for other circuits.
disconnect the ignition switch.
Remove all fuses from the fuse box.
Disconnect the fan motor.
Disconnect the regulator.
Place the kill switch in the off (no start) position.
Connect the battery terminals.
With a voltmeter, test for voltage at any of the black wires disconnected. The regulator would probably be closest.
There should be NO voltage. Not 8 volts, or 5 volts, NO voltage.
If there is, you have a harness problem. If there isn't, start plugging components back in one at a time until the problem presents itself.
Be aware, if the problem returns by installing a fuse, you'll have to start the process all over again on THAT circuit.
Since you have everything off already, this part should go rather quickly.