Looks like this may be resolved with a repair install. TBH, the repair install wasn't without problems.
Just before the second login screen, when Windows sets things up, the message "this takes longer than expected..." appeared. It took some time for this message to disappear, roughly 30 minutes. I then noticed I couldn't click on anything on the start menu, it was all greyed out.
I decided to reboot the system. After logging in the desktop wouldn't show, but I could get to the task manager so I used it to open msconfig to boot into safe mode. In safe mode no problem somehow occured. To be sure I wouldn't end up with the same issue I configured the system to do a clean boot. After the reboot the desktop showed, after enabling everything again the desktop still showed. My only guess why did occured would be memory corruption in user mode.
After the desktop issue was gone, I started with SFC and chkdsk just to ensure no problem was found. SFC didn't find a problem, chkdsk was run twice (first one made corrections and I wanted to be sure no changes were made), ran Windows Update and SFC & DISM again without issues.
Background:
I read these threads for more information about the COMPONENTS hive.
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Dreaded 80073712
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Restoring a Backup of the COMPONENTS Hive - What are the issues?
Somehow I couldn't make the connection between the 'Windows Components store' and the COMPONENTS hive, I basically knew nothing about this file. After reading the first thread I checked if the size issue was the same with my issue which it, unfortunately, was, basically an empty hive.
I booted into a WinPE and used Macrium a few times to restore backups to see if any of them had a more realistic size. I found 1 from mid july, unfortunately I couldn't use it because of system changes (thanks Niemiro for detailed descriptions) so I used my most recent backup (16-sept) and performed a repair install using a fresh ISO.
