You probably can't boot without the USB because you don't have Clover installed properly.
F4 will extract the raw DSDT/SSDT file to /EFI/EFI/Clover/ACPI/Origin so you could patch them later after you boot
The EFI partition will mount when you install Clover, however it'll only mount it the one time. After you reboot, it'll be unmounted.
If you need to access the EFI partition, use Clover Configurator 4.25.
If you're installing El Capitan, I have all the patched DSDT and kexts in my El Capitan guide.