Often this is caused by the regulator getting a low voltage on its sense wire. That's normally the black wire. Voltage drop in the electrical system from the battery to the regulator means the regulator is trying to get its sense voltage up to (guessing) 14v. If you have 2V of drop between battery and regulator it will be trying to charge the battery to 16v.
I have installed a small relay to connect the regulator directly to battery + with key on, powering the coil from the black wire, when there's a large voltage drop and resolving that is not successful.
But with a new harness that's not so likely as it is usually from corroded bullet connectors.
Also confirm your ground is really ground, measure from frame to regulator ground. A bad ground affects charging, raised voltage on the ground works the same way as a drop in plus.
Could still be a bad regulator of course... test, if you are getting 17V at the regulator black, if it's still powering the field coil. It shouldn't be.
