After upgrade to HighSierra Finder's Sidebar do not work anymore
Two things could be going on here:
1
First with the introduction of macOS High Sierra you can now synchronise your Desktop and Documents folders with iCloud Drive.
macOS does some screwy things with them as officially they are actually still in /Users/{username}/(Desktop|Documents) which you'd expect but Finder relocates them into iCloud Drive if you have this feature enabled, this could be why your old shortcuts aren't working.

If this isn't something you want you could disable this by going to System Preferences &gt; iCloud &gt; iCloud Drive and unchecking &quot;Desktop &amp; Documents Folders&quot;
2
The system update didn't go quite to plan, this is the route of trouble shooting you've already been testing and the work you've done so far is perfect.
2a
Next steps assuming it's not just what I've said in option 1 above, would be to create a new user account, and see if that resolves the issues. If it does you can use the /Users/Shared folder to transfer all your files manually, but you will need to re-setup all your preferences and some software may have only been licensed in that user account, not across the system, but from what you've described you seem pretty technically competent and would be able to manage that, if not come back and we can give you further help.
2b
If that also didn't work you should backup your files manually, and perform a full system restore, there are instructions on Apple.com here:
macOS Sierra: Erase and reinstall macOS
The instructions are the same for High Sierra.