how about cleaning up you Apache2 configuration file? replace this lines:

PerlModule ModPerl::PerlRun
#Alias /perl/ /var/www/perl/

ScriptAlias /cgi-bin /var/www/cgi-bin/
ScriptAlias /perl/ /var/www/perl/

<Location /perl>
   allow from all
   SetHandler perl-script
   AddHandler cgi-script .cgi .pl
   #PerlHandler Apache::Registry
   #PerlHandler Apache::PerlRun
   PerlResponseHandler ModPerl::PerlRun
   Options +ExecCGI
   PerlSendHeader On
</Location>
   
<Directory /var/www/perl>
   allow from all
   Options +ExecCGI
   #AddHandler cgi-script .pl
   #SetHandler perl-script 
   PerlResponseHandler ModPerl::PerlRun
</Directory>
[download]

with only this:

PerlModule ModPerl::Registry

ScriptAlias /cgi-bin /var/www/cgi-bin/

<Location "/perl">
 SetHandler perl-script
 PerlHandler ModPerl::Registry
 Options +ExecCGI
</Location>
[download]

as far as i can tell, the directive shown below is telling Apache to serve content from /var/www/perl as CGI using mod_cgi and because it's written before the mod_perl settings it takes precedence over those, ignoring them:

ScriptAlias /perl/ /var/www/perl/
[download]

also, may i suggest that you get in the good habbit of Debian/Ubuntu W.R.T. setting up Apache2 servers? that is create a file in /etc/apache2/sites-available with your settings and enable it using this command

a2ensite myproject && /etc/init.d/apache2 restart

that way you can exclude parts of your configuration in case you need to debug your Apache configuration. more info is in your /etc/apache2/README file.

:)))))