When i want to run perl files out of /cgi-bin i add these

<Directory /var/www/html/cgi-bin/>
Options Indexes FollowSymLinks
 AllowOverride None
 Order allow,deny
 Allow from all
 AllowOverride None
 Satisfy Any
    Options +ExecCGI
    AddHandler cgi-script .cgi .pl
</Directory>
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This may give you a clue as to what to add

Then from the command line i also run

sudo a2enmod cgi
sudo apache2ctl restart
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