The hard thing about merging the files, is dealing with duplicates. Making direct copy and paste actions can be done really quickly through scripting or using rsync on *nix. rsync has an option to update a destination and append shorter files. You can also limit rsync into specific directories and might be a good trial path for you to head down. If you want the security knowing your conf files are 100% correct, I don't think you're getting around doing it by hand.
