I had an awesome time presenting Building your own custom REST Services and consuming them with jQuery AJAX in the Australian SharePoint Conference 2012. A big thank you to the developers that came and geeked out with me for an hour on a Wednesday afternoon.
When you build a custom WCF Service using the CKS template, it is deployed to a subfolder the web front end's ISAPI folder, which, in turn, is mapped to the site's /_vti_bin/ folder.
It appears that in my earlier attempt to create an incomplete version of the REST service template item, I interfered with how CKS's templates worked - and correct features for deploying the WCF service is no longer being included in the package. While existing items were updated and deployed, the new WCF service that I was creating wasn't being deployed to the ISAPI folder.
I've removed the REST template item from my Visual Studio .NET environment, and voila - the WCF services deployed nicely once again.
So that's one mystery resolved. Now I scratch my head about how to fix my VS.NET REST template item.