I know what you mean, I had trouble with the compare feature too. For the most part the only thing that needed to be added to the majority of templates is the small shadow at the bottom of each section (or table), the html code is:
HTML Code:
<div class="dcc"><div class="dcg"></div><div class="dcd"></div></div>
that gets placed at the closure of a lot of tables in the templates. But some templates do have other stuff added to them.
I also found that I had to edit the navbar template since the navbar links are removed from it for this style and put into
header instead. The upgrade restored navbar.