You can remove those characters in the index.php file right at the top. Not sure how they got there..
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "
www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd
">
<html xmlns="
www.w3.org/1999/xhtml
">
<head>
I am not a flash user, so i have no advice on how to integrate. You should be able to enter your flash code into a new module with the editor turned off and then publish the module.
Lookin' good so far.
Mike