I am carrying out some work on a website that is a PR2 with a few good quality, relevant backlinks (PR4-6). It has a presence on Twitter that is updated regularly, a Google Places listing, and listings on some decent directories (Qype etc). The site was rebuilt into Drupal 7 two months ago, with all the basics done - URL rewriting, XML Sitemap submitted to Google, and most importantly, good quality, structured content.

I've noticed that Google is still showing "old" URL's from the previous version of the site that was ditched 8 weeks ago. I think the site may be penalised under the Penguin update, as a previous SEO company created many low quality links from link farms/directories.

My question is what the correct way to deal with this is.

Bing Webmaster Tools can "disavow" links, and I guess I can attempt to contact the link farms to have them removed. I've already submitted a request to Google to request that we have the penalty removed as we're trying to tidy up a bad history. We submit updated sitemaps to Google and Bing daily, and have built some further decent quality, relevant links.

Is there anything further I can do?