Shepherd - 1:40 pm on May 16, 2013 (gmt 0)
why don't you try an redo the home page completely and see if it will recover?
first, this test site was started after the most recent penguin *known* refresh/update (october 2012) so it technically should not be affected by penguin. That said, it does display the same ranking characteristics of sites that we have that were *presumably* affected by penguin.
second, it's my belief that whatever causes the target page not to rank (penguin or something else) has to do with inbound links and not on page factors. Something like: if (page) has x% of inbound links using (target keyword) as the anchor text then (page) will not rank for (target keyword).