I would reverse your approach: First get a scene with some geometry working with the Rift only. Just ignore Leap. Once you have that running add more geometry to the scene, but only control this added geometry with Leap. Then you always have a working reference.
Also use world coordinates on all geometry, so you can easily compare them in the debugger or log files and see if they make any sense at all. And this enables you to use the same projection matrix to render all geometry in a similar way in your shader code.
