The config.plist in the Clover EFI folder on the USB is known to work or you could not have booted the installer USB. Needed kexts were included in the kext folder on the USB.
The SSD/HDD needed boot files to be installed, which you did by running the Clover pkg file, but the default config.plist in the install pkg often has additional items not needed by your hardware and some may even interfere with your system booting properly. It also does not contain any kext files in the kext folders. So, by replacing the EFI folder installed by the Clover install pkg with the one on the USB, you are hopefully assured of being able to boot from the HDD/SSD. Once able to do that, you can run MultiBeast and install your kext files to System/Extensions for FakeSMC and networking and then get audio working and WiFi if you have it. Once that is complete, the kext files should be removed from the EFI/Clover/kext folders so you do not have 2 driver files interfering with each other.