The DIV wrapper id's probably close in the footer so if you delete the DIV's from the header, you'll need to locate the closing DIV's in the footer and remove them as well.
As for adding a flash header, the article below should give you enough information on how to use the embed feature.
http://www.alistapart.com/articles/flashsatay/
The following coding needs to remain in the header, however:
Code:
<!-- content table -->
$spacer_open
$_phpinclude_output