You can't go wrong if you unplug any existing HDD before proceeding with install to USB.
Here is a step by step for making full install USB's:
https://askubuntu.com/questions/1217...e-step-by-step
Perhaps at this point you can just reinstall GRUB to your bootable USB from a Live USB booted in UEFI mode:
Code:
sudo mount /dev/sdxY /mnt
sudo grub-install --boot-directory=/mnt/boot /dev/sdx
Where x is the USB drive letter and Y is the partition number.
Confirm that the existing EFI partition is not referenced in fstab, if it is # it out.
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