Trying to Update Windows 10 to 1703 Error Code 0x80070003-0x20009

I downloaded the ISO from MSDN and tried to update my Anniversary (1607, Enterprise 64-bit). After the initial reboot, it always says it failed because:

The installation failed in the SAFE_OS phase with an error during PREPARE_ROLLBACK operation.

I Googled all around and tried all solutions found but to no avail. I've even tried all solutions found for the same error code for Windows Update and Windows Store! Also all results that Google provided me with have an error code of 0x80070002-0x20009 but mine is 0x80070003-0x20009.
Because I have heavily customized my system (nothing deep into, just bunches of links and themes that I'm extremely sure not to be the cause) so it's highly impractical to do a fresh install. Can anyone help? Thanks in advance.

Edit: Fixes I've tried by far:

• Create a temporary Adminsitrator account and try to update from that account
• Configure a clean boot in msconfig.exe (and in Safe Mode as well)
• DISM.exe /Online /Cleanup-Image /RestoreHealth and sfc.exe /scannow in an elevated Command Prompt (Both told me there's nothing wrong)
• Remove a secondary HDD (Primary is an SSD)
• Get rid of extra EFI System Partitions and a secondary Windows 7 installation partition (and its BCD entry). Currently there's 4 partitions on my primary SSD:

1 ESP BOOT    FAT32 400MB
2 PRI Windows NTFS  158GB
3 PRI Data    NTFS   10GB # For personal files
4 PRI ubuntu  ext4   64GB # 16.04.1 LTS, UEFI boot from #1 ESP

• Download some Windows Diagnostics packages from MSDN and diagnose with them

I find that it could be because of your bios settings. Re-enable CSM and set IGFX as your first option. Otherwise I have always had troubles upgrading windows 10 installs without setting these options back.

Make sure CSM is enabled and set to Windows to boot otherwise you will never finish the install. Also Make sure PCI devices are disabled and just IGFX is set to work and do this also inside windows by verifying its not seeing your PCI graphics and using the intel graphics.

Also, more importantly, your windows boot option should be the first one, just in case you are using bootloaders from other drives. Double check that windows boot is the first option to boot.

Also I noticed that it creates a windows.old folder that will be a duplicate of your original windows folder. So make sure you have at least double that space available for the copy/backup of that folder.

Also disable/uninstall any virus checkers. Try the disable method first, just go to Task manager and disable them on startup and make sure they dont load, and turn off their protection schemes as well, etc, anything that loads at boot time or before other things boot ( to catch malware this is needed ) Theres several excellent virus utilities out there that lock down the system in ways that block updates or copying of files etc.

If you want to go a step further, disconnect any other sata cables just to make sure it wont boot to anything else or a drive cause a problem as it did in earlier installs of windows 8.

These settings have worked for me with all major updates which are basically new installs of windows. Creators update just installed doing this.

Also before doing any kind of update like this its highly recommended by me you do a full clone of the original disk. And after you have had alot of screwups to revert the clone and start fresh back where you were. There could be something happening with alot of partial installs that will make your install unable to ever upgrade again, files not rolling back properly or corruptions happening or partial upgrades happening, etc.

I hope this writeup helps someone, as the endless east-indians with thier generic "just run sfc/scannow" and "use the windows repair tool" are absolutely useless in actually getting installs to work and interpreting errors causing rollbacks or other issues.