You explained pretty much everything on what happened and your reaction to that update since last year. You have done quite an extensive work on design and content but penguin update usually refers to the links that are pointing back to your website.
I quickly get in to your link profile and found tons of links that are coming from blog comments or article websites. Here are few of the examples…
- http://www.science20.com/news_articles/3500yearold_mummies_prove_ancient_origin_heart_disease (Keyword used: the therapist)
- http://www.searchenginejournal.com/microsoft-to-revamp-msn-portal-to-fully-integrate-bing/11263/ (Keyword used: the therapist)
- http://www.fatmanunleashed.com/weekly-check-in-31-body-fat/ (Keyword used: the therapist)
What you should be doing?
- Remove as many links to irrelevant sites as possible
- Try not to get link with exact match anchor text
- Say a big no to links that are coming from Blog Comments, Forum Signatures, Article websites and more.
My advice here is to audit your link profile in detail and see how many bad links you can remove and at the same time build as many quality links as possible. Submit the Reconsideration request to Google and you probably will be get your rankings and traffic back.
Hope this helps!