Boot from your USB and when you get to the desktop download and run
EFI Mounter and mount the EFI partition of your USB.
Copy the entire /EFI folder from the EFI partition of your USB to the desktop.
Eject the USB.
Run EFI Mounter again and mount the EFI partition of your HDD.
Delete the entire /EFI folder from the EFI partition of your HDD.
Copy the /EFI folder from your desktop to the EFI partition of your HDD.
Restart
You should now be able to boot from your HDD in the same way that you could previously boot from your USB.