It doesn't sound like you are doing the wrong thing -- sure, using a true database would be a better way, but there's nothing drastically wrong with what you are doing, except that searches will be long (though that could be sped up by running every so often an external program like htDig which can optimize a text search across a large number of files), or in some cases, impossible to do, but from your description, you're not looking to do these types of impossible searches.

As for modules, you're pretty much looking at the standards that come with any perl dist: CGI.pm particularly.

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Dr. Michael K. Neylon - mneylon-pm@masemware.com || "You've left the lens cap of your mind on again, Pinky" - The Brain