Using Gareth's suggestion of the T4 toolbox I was able to load in a T4 template, but it wasn't generating the file as expected.
What I ended up doing was creating a stub C# class project with my templates, and running a post-build command to copy the output to the WiX installer. Below is a working example.
WiX + T4 example
Here is a quick-and-dirty scripts that walks a folder structure and includes everything but whats in excluded files. It's at least a good starting point for adding files to your project on a folder-by-folder basis.
GetFiles.ttinclude - Utility methods to walk directory structure and maintain list of files
Files.tt - Generate WiX include