Since you now are back on track and are interested in a secure transfer and login method then we might as well change the topic to ssh. ssh replaces both ftp and telnet and all communication is encrypted. Of course you may have other reasons for wanting to allow anonymous FTP access. If it's just you, and other users that you want to allow a higher level of access for (telnet for instance) then all you have to do is run the ssh daemon (I'll bet it's running right now on your Slack box).
From the client side you would use the "ssh" command instead of "telnet" to connect to your machine. ssh has far more capabilities than both telnet and ftp have. For file transfer you have several client commands that you can use "scp" (secure copy), "sftp" (secure ftp, works much like regular ftp), and more. You also can also do graphical file transfers to/from your server using the KDE or GNOME file managers (Konqueror or Nautilus).
If you have to use Windows (I can't imagine having to) on the client side you can download and install the Windows versions of the command line clients or there are several graphical clients that you can install and use. If you have ever used WS_FTP then you will like WinSCP:
Screenshot:
http://winscp.sourceforge.net/eng/scree ... mander.gif
Main site:
http://winscp.sourceforge.net/eng/
Many other Windows based tools can be downloaded here:
http://www.openssh.org/windows.html
Main OpenSSH site:
http://www.openssh.org/
Whether you use telnet/ftp or ssh I would also not allow connections from just anywhere. First off I would never use telnet/ftp over the internet anymore as you know but even for ssh I restrict access down so connections can only be made from specific addresses or address ranges, if you can.
Also, since you are behind a firewall most of your ports are not open to anyone on the internet. I assume that they are open to anyone else on campus though and for that reason I would turn off any services that you are not using. See your nmap output to see what ports are open and shut down any associated services that have those ports open that you do not need. Restrict access to the ports that DO have to stay open to the addresses or ranges that need to connect (you can use iptables for this or in some cases TCP wrappers). The fewer services that are exposed the fewer possible holes will be available to be exploited. Just remember that you could be hacked from your own network, all it would take would be a bad apple, or another system on your network that has been exploited and used as a hopping point.
Ok, now that you have only minimal services exposed on your system and have those select services restricted to specific addresses you would want to make sure you keep those services updated with any security updates. And of course you have to have those services securely configured (use good passwords, etc, etc).
If you want to take it to the next level you might want to do intrusion detection using various tools like snort, tripwire, etc, etc. It all depends on how paranoid you want to be. I don't think you can be too paranoid but obviously to have a very secure system it can take a lot of work. Security is a process that is ongoing.