The stock subs on the 2007 Mustang only require 5v to turn on. The 12v from the Opus was making them pop.
After I installed the regulator the pop was gone.
I've almost got the noise from the doors subs figured out. It has to do with the placement of the RCA connectors. I can move them back toward the rear of the car and seems to work.
Still no idea on the sleep with the Opus 120. I removed the low power jumper, but that just shut down the computer about a minute after it went to sleep.