Not a Perl problem, but the simple solution to the JS problem is to remove the function definition so the window.open method executes inline:

print <<END_JS;

<SCRIPT LANGUAGE="JavaScript" TYPE="text/javascript">
  var url = 'http://perlmonks.com/'
  var mywin = window.open(url,"win","toolbar=0,location=0,directories=
+0,status=0,menubar=0,scrollbars=0,resizable=0,width=520,height=350")
</SCRIPT>

END_JS
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You might want to check out Here document formatting