environment.pl doesn't do much, it lists environment variables and their values, but I tested with many other scripts we have, such as language change scripts, survey engines, w3c validator, etc.. all results in the same error at the same iteration.

Modules listed bellow

LoadModule access_module modules/mod_access.so
LoadModule auth_module modules/mod_auth.so
LoadModule include_module modules/mod_include.so
LoadModule log_config_module modules/mod_log_config.so
LoadModule env_module modules/mod_env.so
LoadModule setenvif_module modules/mod_setenvif.so
LoadModule mime_module modules/mod_mime.so
LoadModule status_module modules/mod_status.so
LoadModule cgid_module modules/mod_cgid.so
LoadModule dir_module modules/mod_dir.so
LoadModule alias_module modules/mod_alias.so
LoadModule rewrite_module modules/mod_rewrite.so
# IMPORTANT NOTE re autoindex_module: we don't want to turn on Indexes
+,
# but if we don't load autoindex_module, a 404 message is given (no in
+dex.htm[l], instead of a 403 forbidden!
LoadModule autoindex_module modules/mod_autoindex.so

# Load WebLogic's proxy module
LoadModule weblogic_module modules/mod_wl_20.so

# Load PHP 5 module
LoadModule php5_module modules/libphp5.so

# To use PHP uncomment the following lines
AddType application/x-httpd-php .php
AddType application/x-httpd-php-source .phps

# Load LDAP stuff
LoadModule ldap_module modules/mod_ldap.so
LoadModule auth_ldap_module modules/mod_auth_ldap.so

<IfModule mod_perl.c>
    PerlModule ModPerl::Registry
    PerlModule Apache::compat
    PerlModule Apache::ServerRec
    <Files *.pl>
        SetHandler perl-script
        PerlHandler ModPerl::Registry::handler
        Options +ExecCGI
        PerlOptions +ParseHeaders
    </Files>
</IfModule>

<IfModule mod_cgid.c>
#
# Additional to mod_cgid.c settings, mod_cgid has Scriptsock <path>
# for setting UNIX socket for communicating with cgid.
#
Scriptsock            logs/cgisock
</IfModule>
[download]

Personally, I never studied mod_perl and perhaps all our scripts are using legacy CGI modules. I think i need to read up on this. Should only one of mod_perl or mod_cgid.c modules be loaded? I have disabled mod_perl currently, and I am re-running the test. Updates to come shortly.

The test proved unsuccessful with mod_perl disabled. Perhaps the next steps for me to take would be to look into migrating all our scripts to use mod_perl and disable mod_cgid.

Huge thanks to everyone for their collaboration so far!