VR stereo rendering with Instancing
While this MSDN page does claim that SV_RenderTargetArrayIndex can be written in a pixel shader, I believe this is incorrect. Viewport array index and RT array index values are both intended to be output by the geometry shader stage. They can then be read by the pixel shader (and have a constant value per-primitive, based on the GS output). However, it is not possible to set these values from the pixel shader.

The stereo instancing approach detailed in those slides is interesting precisely because it avoids using slow geometry shaders. However, if you're not using GS, you can't use multiple viewports or render target arrays. That's why the stereo instancing approach uses one large viewport and bakes each eye's viewport transform into its projection matrix, and requires clip planes.

Clip planes should work, so if you're having problems with them, you could post another question detailing the specific issues (preferably with screenshots) and we can try to figure that out.

(For completeness, note that if you're using OpenGL, the GL_AMD_vertex_shader_viewport_index extension is available on recent GPUs from all three IHVs and allows setting the viewport index from the vertex shader.)