I switched from a shared hosting to VPS and now on webmaster tools it shows there are almost 1,000,000 links from my own site? Is this because the shared hosting account is still active and will deleting that remove the links? I just went down in pagerank and have a feeling that had something to do with it. Any help or advice would be greatly appreciated.
Well Im not sure where they are coming from but I have something semi similar. I currently have shared hosting and my webmaster tools is showing 700 links coming from me. Not sure why it picks up backlinks from myself.
By changing your IP address to the new VPS account, all requests to the old site should end once fully propagated. Providing the identical file structure was moved as a whole, you should not have picked up any additional links. You may want to look at your robots.txt and htaccess to make sure dynamic pages are being dealt with accordingly.
Somehow that would be good if all the links which is connected to your site is relevant. But if not it is like spam. For me proper optimization and link-building could fix it again.