I launched a site 1.5 years ago. At first it spidered very well. Then over time it has slowly drifted back into the SERPs. I have been advised that this may be because I have been penalised by google for having duplicate content. One reason I may have duplicate content is that I only recently realized that my 'beta' versions of my site where being crawled. I have since learned that I should atleast put a disallow robots on directories I do not wish to have spidered and I actually have removed these directories all together, but the fact remains that some links to these pages still exist in the SERPs. Another issue is that I recently moved the site to a new host. On the new host I had to create this site as an addon domain...meaning I had to first create a subdomain of the first domain I setup there and then configure it so that full domain points to the subdomain. Anyways, what I am getting to is that before this was completely set up (which took 1.5 weeks atleast), the site was crawled with the subdomain address. Now it has been crawled with the full domain as the address, but there are still many instances found within SERPs that show the subdomain.
So my question is, what is the best way to tackle this mess? What are my options? I have been told to try something like copyscape (which I have, yet I am still unsure what exactly I am supposed to do). Any assistance in this matter would be greatly appreciated. Thanks!