well, i wanted apache to run all cgi under mod_perl

That's not feasible in any real situtation. CGI is still necessary, both for misbehaving Perl programs that don't play well with Apache::Registry, and for non-Perl programs!

Remember, Apache::Registry (what most people call "running under mod_perl") is just a tiny bit of mod_perl, and it has very explicit restrictions to accomplish its task. You're definitely not even touching the power of mod_perl until you learn to plug in some more advanced structures, like Apache::Template or writing your own handlers.

-- Randal L. Schwartz, Perl hacker