Use Ctrl+h to show hidden files. Copy the ones you know you need. Keep the ones you don't think you need as a backup on the old pc (they may come in handy if you missed something).
Hidden folders simply have a dot in front of the name, so the folder Stuff would not be hidden but .Stuff would be.
To get the permissions correct use your account to copy paste them, that way they inherit your permissions.
Or you can use this command:
This will make you the owner of the folder /home/me/example/. That way you have permission to access and modify everything inside.
sudo chown -R yourusername /home/me/example/
EDIT: All your firefox settings are saved in .mozilla
You can view saved passwords and usernames under >Edit>Preferences>Security>Saved Passwords>Show Passwords