Perhaps you can check out CGI::Simple. It loads and runs much quicker than CGI. tachyon appears to have written a nice alternative that is a drop-in replacement for CGI.pm. You can read a comparison at http://search.cpan.org/src/JFREEMAN/Cgi-Simple-0.04/cgi-simple_vs_cgi-pm.html.
Also, are you using ISAPI, or is IIS relying on the file association to load Perl? If the latter, you may wish to switch to ISAPI for improved performance, but you'll lose taint checking.
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