You could take a look at the
FTP Client library, made available under the GNU LGPL, if you are determined to use FTP and don't mind writing a
java program to do it.
Alternatively you could use the Trivial FTP (tftp) client for linux if you can find a Trivial FTP daemon (tftpd) for your win2k box but be aware that tftp is rarely used any more because it's a bit of an open door.
However, if I was you I would dispense with using ftp. It's basically insecure. See
here for an explanation.
I would recommend instead that you research two subjects. Firstly, Secure FTP, and secondly, Host-based Authentication using SSH. Using the latter you can set up trusted hosts, ie, set up a relationship of trust between your Linux server and your Win2K server, and having done that you can use the sftp (Secure FTP) tool to transfer files in your scripts using a variety of command-line options very easily.
HTH.