Tightening all the control arms and replacing the rear track bar with the Teraflex Monster rear track bar took the weirdness out of the Jeep's handling. We also replaced the OE rear swaybar with an '08 JK Unlimited OE swaybar that's .750 in diameter. That keeps the JK under control when the front Rubicon SmartBar swaybar is disconnected.
But, TrailRunner has a noise. It's the same sound a power steering pump makes when it's failing, but the pump is fine. Spending time around and under the Jeep with a stethoscope hose led me to the conclusion that it's the torque converter.
This isn't an issue for TrailRunner, as there are big plans in store for it.