Need advice about prefered domain setting in Google Webmaster Tool

Question. I have a site that was originally custom built by someone else. We`ll call it http://example.com. We rebuilt the site and renamed the pages and page URLs and now the domain has "www" so it reads www.example.com. All of a sudden, Google is no longer crawling the new site. We just discovered in Webmaster Tools that we couldn`t set the preferred domain for this website to "www" because the other version without the "www" was unverified in Webmaster. We just verified it and set the preferred domain to "www.example.com". Could this have been the reason? Anything else we should try??