The EFI partition is the boot partition on a UEFI booting operating system. You only need one of them, not one on each GPT disk.
From a rescue disk you can use diskpart to prepare the disk
diskpart
list disk
select disk # (where # is the number for the large disk)
clean
convert GPT
create part primary
list part
select part # (Where # is the partition number, should only be one)
format fs=ntfs quick
exit
Then reboot