Now I've got brain-frazzle.
To date, all that seems odd is that the swf object code is located inside the topNavigation div, (which is inside the navWrapper div).
Also you say you have two swfs, and the code only references one.
Was there originally a div container for the swf object(s) inside the contentWrapper?
There is also an empty div 'boxshots' inside the 'products' div, along with the 'lt2m_girlsback_lg.jpg'
Do you have an original 'out of the box' homepage that this can be compared to?