two hints if you decide to rewrite your app and if you want a good cgi:

• use taint mode
• add a apache mod_perl AND a cgi configuration, e.g. 127.0.0.1/perl/script.pl runs your script in mod_perl, 127.0.0.1/cgi-bin/script.pl in classical cgi environment.

developing in cgi has some advantages (you see performance problems better, you don't have to restart apache) but you also should test mod_perl regulary.