There is no way of knowing that your issue has anything to do do with
the ill-described issued in this report from 2 years ago, but whatever;
from your logs it is clear there is at least a bug in grub-installer.

Sep  1 17:27:22 ubuntu grub-installer: Skipping unreadable variable "Boot0000": 
Input/output error
Sep  1 17:27:22 ubuntu grub-installer: Skipping unreadable variable "Boot0001": 
Input/output error
Sep  1 17:27:22 ubuntu grub-installer: Skipping unreadable variable "Boot0004": 
Input/output error
Sep  1 17:27:22 ubuntu grub-installer: Could not prepare Boot variable: 
Input/output error
Sep  1 17:27:22 ubuntu grub-installer: Installation finished. No error reported.
Sep  1 17:27:22 ubuntu grub-installer: info: grub-install ran successfully

There was an error writing to the UEFI firmware variables, yet that
error was not propagated up to the installer to automatically generate a
failed install report.

Can you run sudo efibootmgr -v and post the output?


** Package changed: ubiquity (Ubuntu) => grub-installer (Ubuntu)

** Changed in: grub-installer (Ubuntu)
       Status: Incomplete => New

** Summary changed:

- 15.10 - 17.04 fails to install GRUB on Microsoft Surface Pro 3 & 4
+ grub-installer fails to notice when setting EFI variables fails

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https://bugs.launchpad.net/bugs/1518426

Title:
  grub-installer fails to notice when setting EFI variables fails

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