If you decide you don't want to do all the heavy lifting in your perl code you might take a look at using Unison. I found it to be a nice, cross platform tool for providing automatic "backup" to remote sites over a network.

Also, for a good concise read that includes lots of excellent background information look here. You'll find pointers to perl scripts for backup including one that I modified and used.

Cheers

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Nothing is too wonderful to be true
-- Michael Faraday