Thank you so much!
End result:
/opt/retropie/configs/all/autostart.sh
sudo bluetoothctl remove 40:1B:5F:BA:D5:A0 sudo timeout 6 bluetoothctl scan on sudo bluetoothctl connect 40:1B:5F:BA:D5:A0 sudo bluetoothctl trust 40:1B:5F:BA:D5:A0 emulationstation #autoNow I can easily pair my controller back to the Pi on system startup without even having to plug it in using USB and navigating through all of the menu options.
So happy! :)