I'm not following. Why can't you "pre-empt" the access and authentication? A mod_perl access handler can run for static files, CGI scripts, PHP, etc. It's a standard phase provided by the web server.
I think you are overestimating how easy it is to do your own CGI. You can try copying some code from one of the perld HTTP daemons on CPAN, but there's a lot to deal with in terms of proper error handling and security. Better to let mod_cgi do it if you can.
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