If you have physical control of the servers, you should be able to get access to the server, and change the password. A live Linux CD or DVD should get you full access to the file system. You can then copy the system off with or without changing the passwords.
Does the system create backups? If so, you should be able to restore them to another system where you do have Operating System Access.
As your site has server side code, you will be limited in how much you can rip. Some of the web site testing tools will capture the content from the pages they test. This might get you on your way, and build some test scripts at the same time.