Is it necessary to remotely execute the perl script at all? Perhaps a better solution would be to set up an automated task on the remote server that periodically runs the perl script in question. This would work nicely if you knew the names/locations of the text files you are trying to edit, and they stayed in the same place.
If it is truly necessary, consider installing
Cygwin and
configuring an SSH server, then using SSH to remotely execute commands.
Almost any SSH client would do the trick in that case, as Cygwin is using recent versions of OpenSSH, providing SSH version 1 and 2 support.
Interestingly, Cygwin also includes a port of Perl (Currently 5.6.1, with 5.8 in testing).
Doug