I just have to take a moment and add that I feel the same thing happened to me. I actually made improvements to the coding on pages, and removed duplicative information sitewide. The result has been a loss of rankings. I'm almost certain there is some kind of "protective mechanism" that sandboxes a site that makes major changes. The changes I made have been mostly to improve site speed, and remove unnecessary links, which make for a much more organized and speedier user experience. That said, I have been able to improve sales even as google traffic declined. I do feel that in the end I will get the rankings back, but it is a little frustrating when you make improvements right out of the webmaster guidelines and lose rankings.