The last step for getting my site up is the cgi-bin, and I have it half-way working (strangely). I can try to access it via my domain.org/cgi-bin, get the proper permission error; but the files within the -bin show up if I access them through the URL. When I login on the frontend, I get a "Cannot Open File at cgi-bin/file.pl". The entire site is built in Perl. I have tried the symbolic links to the -bin, ScriptAlias, and all of my files are chmod 755. (The one's not in the -bin work fine).

The following is in my apache2.conf:

# Include generic snippets of statements
Include /etc/apache2/conf.d/

# Include the virtual host configurations:
Include /etc/apache2/sites-enabled/

# Server Name
ServerName site.org

ScriptAlias /cgi-bin/ /usr/lib/cgi-bin/

This is my /etc/apache2/sites-available/default/ file:

<VirtualHost *:80>
        ServerAdmin webmaster@localhost

        DocumentRoot /var/www/
        <Directory />
                Options FollowSymLinks
                AllowOverride None
        </Directory>
        <Directory /var/www/>
                Options Indexes FollowSymLinks MultiViews
                AllowOverride None
                Order allow,deny
                allow from all
        </Directory>

        ScriptAlias /cgi-bin/ /usr/lib/cgi-bin/
        <Directory "/usr/lib/cgi-bin">
                AllowOverride None
                Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch
                Order allow,deny
                Allow from all
        </Directory>
...
    

Was wondering if anyone knew how to properly set up the cgi-bin.

Grr, thought mod_perl might help, but didn't.

EDIT: Officially went through all my code, and it turns out, that the cgi-bin was working fine, but there was a problem with actual code making files. When I moved my files from my old hosting to my VPS, the directories were different, so it was caused by a /dir/ needing to be dir/.

And mod_perl did help, too. Fixed up a different error I was having, yay.