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I ended up figuring it out, but thank you for the reply.
After running SD a few more times, I managed to determine more specifically the areas that were causing it to fail. I then had SD skip those directories (in the /private/ folder, as I thought), and after it finished doing its backup I went back in and copied the skipped directories by hand. Each one had a handful of files that must have been corrupt, but I elected to delete them. I figured that if they were really corrupt then they must not be used much since I've never had any problems.
SuperDuper is great, I'll definitely recommend it!
Michael
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