The UI and selection beam issues are limitations of Unity when it comes to quadbuffer stereo. For the UI, we recommend setting it to world space rather than screen space. As far as the stylus, use a mesh renderer rather than a line renderer.
Ghosting is expected in certain situations, usually intense contrast differences. Say you render full black on the left eye, and black with white dots in the right eye. The white dots will bleed through and be seen by the left eye. This is simply a limitation of the stereo hardware. It's best to manage it from a couple different angles. Keeping objects close to the zero parallax when possible is one recommendation. Another is minimizing visual contrast between the subject and the background via materials, lighting, post-processing, etc.
Also, if the ghosting is related to motion, that may be a different situation. If that's the case, let me know if its happening specifically in the preview window, or if it's happening in builds as well.