Cronjob:
GDatabase.pm could go into e.g. /var/www/localhost/, wwwroot is not necessary.
# 5 0 * * * cd /path/to/qa-scripts/invalid_files/; perl main.pl > /tmp/toparse; perl make_hash.pl /tmp/toparse > /path/to/your/GDatabase.pm

Copy gentoo_unused_files.pl into your wwwroot.
Replace the path at "use lib qw( /home/idl0r );" by /path/where/the/GDatabase.pm/is/

mod_perl:

75_mod_perl.conf:
<IfDefine PERL>
	LoadModule perl_module modules/mod_perl.so
	PerlRequire "/etc/apache2/modules.d/apache2-mod_perl-startup.pl"
	PerlModule ModPerl::Registry

	PerlSetEnv PATH "/bin:/usr/bin"
	PerlSwitches -wT
	PerlOptions None -Authen -Authz -Access +ParseHeaders

	PerlModule strict
</IfDefine PERL>

Vhost conf:
<Directory /path/to/your/wwwroot>
	...

	<IfDefine PERL>
		<IfModule perl_module>
			# Either FilesMatch or Files
			<FilesMatch ^gentoo_unused_files\.pl$>
				SetHandler perl-script
				PerlResponseHandler ModPerl::PerlRun
				PerlOptions None +ParseHeaders
			</FilesMatch>
		</IfModule>
	</IfDefine>

	...
</Directory>

mod_cgi(d):
The usual way...