I managed to clean up the damage
I used efibootmgr to delete the EFI boot entries on the Windows drive 

I then booted an Ubuntu USB stick, followed Gentoo's guide for mounting and 
chrooting into the Ubuntu environment I needed to fix
https://wiki.gentoo.org/wiki/Handbook:AMD64/Installation/Base


I then did grub-install --target=x86_64-efi --efi-directory=/boot/efi, where 
/boot/efi had my external drive's EFI partition mounted up 
https://wiki.gentoo.org/wiki/Handbook:AMD64/Installation/Bootloader


I checked the drive with efibootmgr to make sure Grub installed right, it did.

This is a really critical bug for any desktop user...

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https://bugs.launchpad.net/bugs/1173457

Title:
  Ubuntu  Installer uses wrong bootloader location for USB UEFI installs

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