I was looking at the scripts included with WP and dont see what I can include to use jQuery UI Auto Complete. What do I use? I tried including the whole jQuery UI from Google CDN and auto complete works but some parts of the admin dashboard fails. eg. Custom Menus
WordPress uses the jQuery Suggest plugin, which existed before Autocomplete was added to UI. You can enqueue 'suggest' to load it if it'll work for your needs.
Otherwise I think you'd have to build a custom jQuery UI download and then just extract the Autocomplete code, otherwise you'll have two versions of things stepping on each other and you'll get the failure you describe.