Assuming your network guys get the X.25 tunneling set up correctly on the Cisco routers, the packet transport should be transparent to your application. You just need an FTP client. TCP/IP hides the hardware layers from your application which is it's purpose after all.
Search PerlMonks for FTP. SuperSearch PerlMonks for FTP. Search CPAN for FTP and SFTP. Looks like Net::FTP, Net::FTP::File, or Net::SFTP should do what you need. I have no direct experience with any of these packages.
These modules should make your application pretty straight forward. There are many posts on this topic and I'm sure this task has been solved many times.
There's never enough time to do it right, but always enough time to do it over...