Shoulda asked me earlier; go edit your /etc/httpd/conf/httpd.conf, find any directives resulting in the building of each site:
Example:
<Directory /home/ugn/public_html>
Options +ExecCGI Indexes FollowSymLinks
allow from all
deny from none
</Directory>
Add in +ExecCGI to the "Options" line and restart apache, you'll now be able to throw perl scripts anywhere you please lol...
To add in the ability for SE Friendly's with shorturls, while you're in your httpd.conf find any "AllowOverride" lines and update the value to "All" (hey, it's your VPS, I'm SURE you trust every hosted site's owner), then just edit your .htaccess in your web root and add in "AcceptPathInfo On".
Mmmm, sweet VPS...