You need to do more debugging to find out if your requests are going through mod_perl or not. For example, you could add a warn of $ENV{MOD_PERL} in your test script and see what shows up in the log.
Nope, nothing in the error log. Apache isnt executing the .pl file, just serving it up as a raw binary file (its not even converting newlines).
> AddHandler cgi-script .cgi If you take that out, does mod_perl work as expected?
No, that just prevents the .cgi files (currently vanilla cgi scripts) from executing. And I've restarted apache after every modification to the configs...(thanks for responding though!)