In README.md in the section describing "Manual Installation," you're missing the line that adds the needed entries in /boot/config.txt. The line that's there now (sudo sed -i '/enable_uart|pi3-miniuart-bt-overlay|force_turbo/d' /boot/config.txt) deletes any previous entries, but fails to insert the proper new entries. From the PiBakery script, I believe this line is missing here:
echo -e '# AlarmDecoder Settings\nenable_uart=1\ndtoverlay=pi3-miniuart-bt-overlay\nforce_turbo=1\n' >> /boot/config.txt
In README.md in the section describing "Manual Installation," you're missing the line that adds the needed entries in /boot/config.txt. The line that's there now (sudo sed -i '/enable_uart|pi3-miniuart-bt-overlay|force_turbo/d' /boot/config.txt) deletes any previous entries, but fails to insert the proper new entries. From the PiBakery script, I believe this line is missing here:
echo -e '# AlarmDecoder Settings\nenable_uart=1\ndtoverlay=pi3-miniuart-bt-overlay\nforce_turbo=1\n' >> /boot/config.txt