Broken system after installing USB qube

I’ve never tried to install Qubes on an external USB drive, so I’ll try to guess the best way to do it. You could boot without usbcore.authorized_default=0 and rd.qubes.hide_all_usb since both won’t work in your case. You could keep rd.qubes.dom0_usb=X in your kernel boot options to attach the controller with your USB drive to dom0, give sys-usb the other USB controller under “Devices” in the settings and use that one for everything USB related.