Ralph_Slate - 8:55 pm on May 6, 2013 (gmt 0)
@purplekitty, keep in mind that it is believed that Google has timed/tiered penalties. You can fix the source of your penalty but maybe Google has put you in the cooler for 3 months, so you have to wait it out.
Also keep in mind that Penguin last ran in October, so if you made changes since then, you may still have an algorithmic flag set on your site. If you made the changes before the last Penguin run, your changes may not have been what Penguin is hitting you for.
I have a theory that you can overcome Penguin issues with pages that have a legitimate backlink profile. When I got hit, my pages that had good natural links to them were more or less OK. My pages without any links were the ones that seemed to be hit. Do you see such a pattern?
I view Penguin as applying a weight around your site, maybe amplifying other problematic issues, or maybe taking away some karma that you've built up. It wouldn't hurt to try and improve the site in other ways - maybe eliminating some thin content, no-indexing pages that don't belong in the index, making sure you don't have forum spam, etc.
I think that it was correct of you to nofollow your cross-owned links. Although I think that Google is being stupid by forcing us to disavow such links because their algorithm is dumb enough to give you a benefit from having them, you don't deserve the benefit either because the links are all made by you.