Just change the port your ftp server is listening on to a different port..........either through config files or command line (whichever works for your server)...
As for iptables, I'm not familiar with the ins and outs of it......................I use gShield to configure iptables and change the gShield config file to open up whatever port I want........in this case to match the port you've got your ftp server listening on...................
Note: You will need to add the port number to the url whenever you try to connect to it, like so:
Code:
ftp://my.ftp.server:XXXXX/
replacing the XXXXX with the port number.........