I think you can use Timeshift to backup just your /home/your-username/ directory and leave the OS files out.
@wizardfromoz is the Timeshift guru, so he can tell you clearly.
/home/your-username/ contains many hidden files and folders, and you may want those... they have configurations of many programs, such as Firefox, Thunderbird, and others. But some of these may save program settings for the apps you're having trouble with too. Can you list the problem apps for us? Or review /home/your-username/ yourself to see if anything looks like trouble. Be sure to look in the hidden folder /home/your-username/.config too. You can save /home/your-username with a simple copy/paste and don't really need Timeshift.