Hi.

Where do you get to reference and create your start.pl (or whatever you prefer to call it) ? I have configured it in the httpd.conf. I can load the start.pl just fine, it preloads the mods correctly.

Not clear as to why you are having that Exec permission on your entire /publlic_html and are making it ScriptAlias :/ The cgi files reside on the document root of the virtual server /home/user/public_html/webmail.cgi That is the only way I can get the cgi to run without 403 errors.
Any special reasons to do so? Additionally, <Location></Location> is what is needed instead of <Directory></Directory> directive... AFAIK. HyTC
When I use the code below, mod perl is not recognized in the admin environment:

<Location /home/myuser/gmail>
SetHandler perl-script
PerlHandler Apache::Registry
PerlSendHeader On
Options +ExecCGI
</Location>