in your /etc/apache2/ directory you will see two directories.

sites-available/
sites-enabled/

for apache2 to pick up a site specific configuration you will need to
create it and save in sites-available and create a link to it in sites-enabled/

the site specific configuration is where you define ScriptAlias or
module specific handler directives.

It sounds like you do not have a handler registered for .pl extensions
so they are being handed to your browser as text files.

So you need to either set an AddHandler directive that maps .pl to the
correct interpreter (installing mod_perl does this automagically)

Or ensure that .pl is handled as a CGI script by putting it in a
directory to which ScriptAlias or ExecCGI applies.

CGI is slower but it is a lot simpler to setup ;-)
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