Since no one chimed in I blew away my setup and started over moving step by step to identify where the audio broke.
The power button configuration was the culprit. The script worked for the power button perfectly powering on and off the Pi but killed audio from the Mifiberry AMP 2. Upon further researching the reason behind the issue was that the Mifiberry AMP 2 uses several GPIO pins to communicate between itself and the Pi3. Of course one of which is the same pin the power button configuration script uses.
I have since tried to modify the script to use a different GPIO pin (GPIO 5, pin 19). The script works to power off the Pi but not on. Further research told me that the script doesn't power on just off and that I can solder in a header or use pins 5/6 (GPIO3/GND) to power on the Pi. Given the Mifiberry, it looks like my only option is to use the header which is doable but I'd prefer to have only one power button that performs both power on and off functions.
Is there a way I can meet my goal via script, resistors, etc given what I have to work with, a long button press for off maybe? I thought about wiring the button to both the reset header pins as well as off function pins (19/20) but don't believe the Pi will know what to do with that input.
Any ideas? Thanks
Here is the link to script I ran from. Here.
Here is the info from Mifiberry.