I have updated this prototype to work with the latest THREE.js and only use one CSS3DRenderer layer, you can view the live demo on heroku rusthon.herokuapp.com. The shading over the CSS3D windows is done with the bloom fx in THREE.js, some of the stock fx are compatible with RGBA targets, and able to render overtop of the interactive HTML layer.
You can drag and drop Collada (dae) files from your desktop onto the view and they will be loaded and attached to the 3D window. See the source code, here. The prototype works in Google Chrome, Safari, new iphones and androids, but not very well in Firefox see this bug webgl alpha overlay css3d bug