I think its clear that Panda appplies a 2 part filter
(1) All your #*$!ty pages get hammered.
(2) your main pages, usually the not #*$!ty ones, get hammered too.
You need to fix a great mahority of the #*$!ty pages, for the non #*$!ty penalty to be removed site wide. Fixing indivudal pages will undoubely see them improve, but youve got to cross that "ive fixed almost all of the #*$!ty pages" threshold to see a sitewide fix.
I have two sites,one penlaised, one not.
both have lots of articles.
both have huge business direcotires, which by any definition, are thin.
Difference is the one not penalized has better(read - totally unqiue articles, not articles based on wikipedia slightly changed) and also, it does not have lots of random content like "4 featured businesses" on every page.
The large thin business directory, seems not to be the major problem, its the article farm/dupe content/lack of unqiue content to the page becuase you are putting content that appears on other pages on every page that is the big problem.
I am rewriting articles as fast as i can and yes, I see indiivual fixed pages rise in rankings within 7 days... am racing to that threshhold.
If you claim to have all unique articles, but still got hit. Take a good hard look at them. Are they articles that are slightly different than what else is out there? Are they on average.... short.... or on average.... 500 words? If so, you need to harden up and take action.