I would disagree with you on the redirection of the old site URLs. I have worked on and consulted with several eCommerce websites and from 2004-2008 ran my own successful eCommerce site called thesprintstore.net. I changed the URL structure and had the same thing happen to my site. At the time I chalked the issue up to moving everything around and believed that the site would eventually bounce back. Due to the economy it never did.
I later discovered that the old URL structure had some seriously powerful backlinks from sites like techcrunch, engaget, engagetmobile and other awesome forums. If I had only redirected all of the old urls to the new urls all of that link juice would have continued onto my site and I would not have experienced such a significant drop in domain and page authority.
Regardless of indexation or how long ago the urls were changed its never a good strategy to play hide and seek with Google so simply apply 301 redirects from the old to the new and see what transpires over the coming months. After all, it cant hurt right?