We have found the issue, someone has some terrible programming that is fetching 100's of MB of recordsets from the SQL server, this is causing some major issues, and we are working to resolve this now.
The site we found was part of the cause, but not all of it, I am doing an iisreset now and continuing to work on Win8, I need to do an iisreset to "reset" my statistics for monitoring, as well as free up some RAM on the server.
In further review, we re-enabled the site causing problems, and the server slowed to a crawl and the problems came back, when the site was not working, the server was very stable.
