The spacing (or lack thereof) on the site is very distracting. The left menu has zero pixel spacing from the content, and so the side menu basically runs right into the content. The table of contents on the right isn't obvious that it's a table of contents for the article, it just looks like another menu of some sort on the right.
I did some quick restyling just to satisfy my curiosity with some notes. I know it kind of makes it looks like wikipedia, but wikipedia is easy to read.
I've added a 'padding: 1em;' to the sidebar so hopefully that deals with your left menu issue.
Looking at your screenshot, I think I like what you did with the table of contents. Could you post the CSS you used to do that? (Maybe it's obvious to you how to do that, but I know very little CSS so it's a mystery to me.)
I did some quick restyling just to satisfy my curiosity with some notes. I know it kind of makes it looks like wikipedia, but wikipedia is easy to read.
http://imgur.com/G5QfOua