I have a couple of notes about this problem.

If you use #!/usr/bin/perl -<options> -- The shell and perl will ignore everything after the -- including the return.

If your ftp (on both ends) is not broken, transferring the files in ASCII mode should fix up the line breaks to be the correct variety on both ends of the link as needed.

Some windows ftp clients see that the remote end is Unix and so use binary mode for everything which, of course, is not the correct behaviour.