Permissions Completely Borked After Using Main Drive in External USB

Hi everyone. This deals with Windows 10 Pro x64 latest version fully updated. I was going on holiday, and was taking my small laptop. I had a lot of files on my main desktop computer drive where Windows is installed (500gb Western Digital SSD) and chucked it into an external USB encloser. When I connected the external encloser to my laptop it said when I tried to open the main folder "you don't currently have permission to access to this. Click to permanently get access to this" which I did and then could access the entire drive and see the contents of it.

Fast forward to now when I returned home, I put the SSD back into my desktop, it boots OK but everything doesn't work correctly anymore. When I click the start button it says "Your start menu isn't working. We'll try to fix it the next time you sign in".
When I try to open a simple Microsoft Word document I opened dozens of times from my desktop, it says "Your AutoCorrect file, blah blah blah could not be saved. The file may be read-only, or you may not have the permission to modify the file."

When I try to open a simple PDF I've opened dozens of times, I get "Adobe Acrobat Reader cannot open inside an AppContainer in Protected Mode due to an incompatibility with your system configuration. Would you like to proceed?
1. Open Reader with the AppContainer disabled inside Protected Mode
2. Do not open Reader due to the AppContainer system incompatibility

And pretty much most other programs are completely screwed up. My taskbar has mostly blank icons now. I did not modify the contents of the boot drive in anyway, only granted permissions for my laptop to access and see the contents of it. It seems the permissions are COMPLETELY screwed up on my main C Drive and I can no longer use this computer properly. Is there anyway I can go back to what it was without doing a clean reinstall? Or somehow disable all the garbage and completely useless security permissions that only serve to take away control from the end user and give me problems like this? I can't even open Settings because my Start menu doesn't work anymore! Any help would be really appreciated!!

I do not have a restore point unfortunately.
The hidden administrator account works perfectly though, start menu and all. Is there something I can do from there to fix my main account?

Create a new user profile, and copy your data from the old to the new.

I guess your laptop has a different account name and you changed the Ownership.
Log in with your account, go to \Users\Name and Take Ownership of it.
Add Take Ownership to Context Menu in Windows 10

Megahertz said:

I guess your laptop has a different account name and you changed the Ownership.
Log in with your account, go to \Users\Name and Take Ownership of it.
Add Take Ownership to Context Menu in Windows 10

Thank you so much for the help. It took hours to run the take ownership script, but things are more or less back to normal. However, with the Start menu, I still get that critical error message...

Give ---dism /online /cleanup-image /restorehealth---a try and see if it fixes any corrupt files.