You hit on a nice topic and Idea here...

First...

One of the issues I find that this site lacks in its navigation is how its thought out

The main Menu Bar Contains...

Members
Stories
Submit
Forums
Links

But isnt Submit a part of Stories, Forums and Links?

The side bar contains

Site News
Story List
Submit Story
Forums
Links
Members
FAQ
Contact ME

Now Story List is the same as Storys on the main Menu bar
Submit Story is the same as Submit on the main Menu bar
Forums is the same as Forums on the main Menu bar
etc
-----------------------------


So my advice is to create a system where either the Top Bar is the main bar, and the left bar is the sub menu

For Example

Click on Links, and you will get a bar that says

Submit Link
FAQ
Contact ME

Click on Stories, and you will get a bar that say

Submist Story
Story List
Story Links
FAQ
Contact Me

Click on Members, And you will get a bar that gives all the menu options

Next Delete all the Submit on the Top Bar

and then you can add the submenu options to the left bar that you just requested...