First off get everything in writing! After the quote, I start out with a proposal where I give a detailed description of the project and then layout the phases with a description for each. After that is agreed upon, contract time. You must have a contract, trust me. Payment amounts, payment schedule, etc.
With that said...
I would move to a more standard based CMS if possible, wordpress maybe since the current format appears to be a blog like setup. If not, Joomla is more comprehensive and flexible.
It doesn't make sense to have two columns (one appearing to be a sidebar) with the same type of content. IF that stuff needs to be there, truncate it. Instead of the full story, it should be a teaser with 'read more...' after it. Visitors will take more time reading more stories this way. Also 580 comments looks nice, but it's ALL spam! Implement askimet if you're going to go with Wordpress.