This sounds like... there should/could be some bash scripting here for reliability etc- rsync might have some features for you, - I know I know.. you're doing all this in perl. Thing is, some of what you talk about- these are problems that have come up for a lot of people, and custom software has been build tried and retested and rebuilt.. for making life easier.

Tell you what perl might be real good for here, holding everything together, maybe with a bunch of system, back tick calls.. etc. This will accept no user input, right?

Anyhow, I would seriously look into using as much of the existing system and shell utilities as possible. That would cut down on a lot of possible bugs.