System Preferences/iCloud/Manage is the official way to do this, but you will find folders for every app you have ever installed. I'm not aware of a correct way of removing them all. If you use the command line cd ~/Library/Mobile\ Documents; du -sk * | sort -rn you will see most of those directories are largely empty. You can always create a new Apple ID and start from scratch :-)

App Cleaner isn't going to touch iCloud data.

Have you considered renaming your Documents folder to something else? As far as I am aware there isn't anything particularly special about the Documents folder. You could have a Documents folder and a LocalDocuments folder and populate as required....

@kakyo - very sorry, the script failed because a tab became spaces - fixed now.

I'm using Fujitsu ScanSnap, but I don't see evidence it causes the problem. I have had it happen whilst logging on, editing mail, submitting a Safari form, and during Time Machine backups (system otherwise idle). I've posted my solution below (monitor and kill if hogging the CPU).