If you're running from the command line on server C, why can't you just ssh into server A where your script is and run from the command line there? The script can also ssh over to server B to manipulate your files. If you set things up with ssh public/private keypairs, you can do it without having to store passwords anywhere. You might want to use Net:SSH in your scripts. It's not clear that there's much perl-specific in the question.
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