Again, thanks for the well thought out advice. I do have a LOT to improve on the ecommerce side of things, and I admit right now I am kind of fishing for possible quick fixes for the Panda situation.
As for the navigation, it is generally one way; there isn't any linking from the ecommerce pages to the articles (blog) except for one link from the home page, but the articles DO link some of to the ecommerce pages.
Is it possible that you are linking within the articles to ecom pages using a pattern of anchor text that could appear "unnatural"?
That is a possibility. The whole purpose of the articles is to try and flow page rank to the ecommerce pages, and to also create a domain-wide level of "authority" for the WHOLE site.