Here is what I would like to do:

I use the news module quite frequently on my site. Say an anonymous user views a story in their browser. At the bottom of the story there are two drop boxes -"nested, oldest first" etc. When a registered user logs in and views the same story, notification options and a slew of other options appear at the bottom. Well duh right? I have no need for these items whatsoever and I want a cleaner look. I just can't seem to find the code so I can comment the lines out. I want all users to not even see comments and notification options when they view stories. Thanks for your help!

All you need to do is to set no notifications and no comments in the module's Preferences.