Thank you all for your insight - good stuff, but still stumped.
Here's everything we know that might help point out why the main domain (ie www.root.com) was penalized by Google. We redirect root.com to www.root.com with a 301 redirect, and it is setup this way in Google Webmaster Tools too.
December 9, 2011 - the site's 404 error page was incorrectly setup as a 200, resulting in a quick bloat of 1 million plus pages. The website dropped from Google immediately. The error page was correctly setup 2 days later. The site still appeared in Google's index via site: query. However the site didn't reappear in Google's SERPs until May 2, 2012.
October 25, 2012 - the website again drops from Google for an unknown reason. We then moved a significant portion of content from www.root.com to subdomain.root.com. Pages from subdomain.root.com began appearing within 3 days as high they appeared previously on Google. From December 9, 2011 throughout this entire time we were correcting any errors reported in Google Webmaster Tools on a daily basis.
February 26, 2013 - The website yet again is dropped from Google, the subdomain.root.com continues to appear and rank well.
Due to moving most of the content from www.root.com to subdomain.root.com, the index for www.root.com from October 2012 dropped from 142,000 slowly to an average of 21,400 ending at today's 4,230. However this index count fluctuates greatly every few days (probably due to moving content from www.root.com to subdomain.root.com).
Of note, the site is NOT a content farm, but legitimate unique technical content that is hosted for hundreds of clients.
Again any ideas are most welcome!