One client's site was hit by penguin back in 2012. The thing is, only some sections (stored in sub-folders) were affected. We already submitted the spammy links pointing to his website (most of which were pointing to the homepage) to the Google's disavow tool, many months ago, but the most affected sections haven't recovered their rankings.
We have modified the site's content, and other changes to make sure its not an on-page issue.
Shall we use link checking tools other than GWT to see if we find more links that could be causing the penalty to stay and submit them as well?
Would it work if we change the sections to new folders, and de-index the current ones? the competition is really low, so starting from zero could be a good option in this case, if so, is there a way I can keep the rankings on Yahoo and Bing?