Not sure what the problem is either, but if you want a plain-old index.html in your webservers document-root and use a .cgi at the same time to do all your processing, you could use a very simple index.html that redirects to your .cgi. Something like this:
<html>
<head>
<meta http-equiv="Refresh" content="0;http://www.example.com/cgi-bin/your-script-here.cgi" />
</head>
</html>