Closing the loop on this for anyone in the future. In the end, I had to:
From the working 4.0 host:
- Enable a local admin + login one time.
- Take a fresh backup.
On the target 4.1 host:
- Restore the backup
- in a dom0 terminal, run "qvm-prefs <VM Name> qrexec_timeout 60000000" <---- number is just a large, arbitrary number so Qubes doesn't shut the machine down when qrexec doesn't come up.
- Boot the machine 3x times. On the third time, Automatic Repair starts.
- Logged in with the local admin.
- Attempted automatic repair - no good.
- Opened a command prompt and used diskpart to assign the boot partition to letter S and the Windows partition to letter C.
- used bcdboot to regenerate the boot files.
- used bcdedit to ensure the correct partition was set.
This *still* failed on the next boot, however I was able to get into Windows Safe Mode. Another reboot had me functioning normally.