Finally I finished moving the non-directory part to WordPress as main content management system for this site. I'm excited, since this is what I wanted to do for long time now. I pointed the most important indexed pages with 301 redirect to the new ones and hopefully we won't have trouble getting re-indexed and ranked again. Please, let me know if there is something wrong or raises concerns about functionality of the site in the comments of this post or in the forums by clicking on Leave Feedback. I appreciate all your help and support.