How to reset default sidebar favourites icons in Finder?
How did you restore permissions? Manually, or did you use the "Repair" feature in Disk Utilities?

Restoring from a Time Machine backup from before things went bad should work. 

One thing you might try before restoring is to delete the Finder preferences. ~/Library/Preferences/com.apple.finder.plist then relaunch the Finder (Hold Option while selecting the Finder icon in the dock). The preference file will be regenerated with the system defaults.