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InformIT.com : Articles > Blueprints for the Web: Organization for the Masses an excerpt/article on card sorting. Registration is required, but free.
Unfortunately while an IA can card sort those kind of numbers, users often start to fade (in my experience) around 200 cards. Luckily it's alos an interesting interactive thing to do, so they'll go longer. If I were you, i'd pay special attention to areas that are giving you trouble, and test with that subset of content.
But I'm happy to hear what others think.