They got 80,000 daily uniques on just 900 links, and those are from directories (i.e. useless)? Are you sure you're looking for the culprit in the right place? There's no amount of directory links that can get you 80,000 daily uniques and I would think if they were not involved in the original ranking, they did not lead to the penalty either.
What were the actual strong links that got them such nice traffic? How were they acquired? That's what I would be looking for.