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The technique I use in editing zone files or otherwise in perl is by having a flat-file database of records to edit, and after every change I would generate a zone file based upon that file's contents.
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That's what I'm talking about too. Create a custom file format for zone records. Edit that when you want to enable a user to customize his records. Then generate a real zone file based on those contents every time he makes a change. It's easier than parsing up a master zone file.