The fight took place, and I think I won!
Here is what I did;
1. I created a save point.
2. I made a system image of the system drive. I had to buy a special external usb drive formated to NTFS (not the usual fat32) and put the image on there.
3. I removed Asus Suite III by uninstalling it through programs & features screen. Then I booted to safe mode and ran the ai3cleaner program thats on the asus forums. It seemed to remove all remaining bits.
4. Then I rebooted and started preparation for doing the big update.
5. I changed the registry entries back so both ProgramFilesDir and ProgramFilesDir (x86) are now back pointing to the C drive. I then exited regedit and noticed immediately some shortcuts pointed in the wrong direction. I also noticed that the windows search bar couldnt even search my computer anymore.
6. I rebooted and ran the media creation tool, which now grabs the current version of windows. I told it to keep my programs and apps and files etc. It then installed over the top and updated my Windows version.
7. After installing and rebooting a few times. The shortcuts seem to work again without me having to edit them. Also the app store is now working again too!
I have noticed that on both attempts I've done the big windows update it seems to uninstall Nvidia's Geforce Experience program. I had to reinstall it. Also it seems to disable SLI configuration. I was able to go in to the control panel and reset that back.
So windows is now updating properly and so far all is going well.
@loonylion
I know what you mean. Hmm interestingly I've just looked at Settings -> System -> Storage, and in the early windows edition I could set documents, music, pictures and videos to point to another drive. They did have Storage listed in the first edition that was greyed out. I've just checked on this version and its been replaced with 'New apps' and that can be set to another drive letter too. I'll let you know how that works out. I've just changed it.
Apparently changing the 2 (or more) registry entries that I did used to be ok on previous windows editions. But it seems windows 10 doesnt like it at all.