No.DOCTYPE declarations are ADDITIONAL to the content-type. If you set content-type to "text/plain" for instance, the browser should ignore any markup in the file and just show it as plain text with funny tags in it.

You need a valid content-type header. Sometimes this is automatically provided by the webserver, but most of the time, it isn't.

Also, you might have uploaded your perl script as binary with different line-endings than the line-endings on the target machine, or your script is not executable by the webserver user (do chmod 755 filename).