I'm a newb so please forgive me. I'm running the apache server that comes with OS X.
Since I posted this question, I found a PHP script that does a download (example that comes with files, etc.) and it worked through the browser. It seems that perl is at issue, and all the headers are just not working.
And I tried the content disposition and content type together, and individually, and the same result happens: it prints the output to the browser.
Basically, you need to enable the ExecCGI option for the directories your scripts are situated in and make sure that executable (chmod +x) files with .pl extension are considered CGI (by using AddHandler directive).