Doing that type of major makeover is better done at the template level considering several of the css classes are hard coded and are difficult to impossible to override in css_additional.css. It will also give you more flexibility as far as doing the exact type of layout you want to do. The downside however is some of the classes will need to be retained. The javascript on the pages relies on these classes to trigger several ajax functions in the threads and that will take some time to evaluate which ones you do and don't need.
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