the div structure should be:
->outerWrapper
->->innerWrapper
->->header
->->navWrapper
->->storeMessage
->->featuredWrapper
->->featuredWrapperAfter
->->contentWrapper
->->footerWrapper
....
the structure on your site is:
->outerWrapper
->->innerWrapper
->->header
->->navWrapper
->->storeMessage
->->featuredWrapper
->->->featuredWrapperAfter
->->->contentWrapper
->->->footerWrapper
the content is not sitting right because it has become a child of the featuredWrapper which it should not be. it looks you have been making changes to the structure of the template that are causing the issue.
I have not touched the template structure so I do have an issue here, could I have a suggestion for a fix.