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The traffic that dropped is engine traffic but it is also from people who were linking to us which makes me think that it must be due to new URLs and file names/ structure.
Have you gone back to the websites that were/are linking to you and provided them with new URLs to whatever pages they were/are linking to? And in doing that, giving them their exact URL and copy of where the link to you resides so that changing it is easier for them? I'm not an expert among these forum people, but it seems like this could a. bring some formerly regular traffic back if it is missing and b. be part of your linking strategy. Even though the redirect is happening, I'd think you still want direct and new links. You could also at that point suggest where else on your pages they could link to, if appropriate for their users/policy. Again though, not an expert.
