Hi Matt-
Not sure that this will solve your problem entirely but:
1. Put your camera as close to the plexi as possible when taking the picture--this will help block the reflections in the first place and also help the camera's focusing mechanism overlook anything on the plexi (scratches, bugs, etc.).
2. Set the aperature, if possible on your camera, to the smallest depth of field possible so that only things in the far distance are in focus.
3. Use a lens hood if your camera can accept one. Many consumer cameras (if they are of the major camera manufacturers) have adapters available that you can buy to attach things like lens hoods, filters, other lenses, etc.
4. Take everything off the glareshield you can--that's why they're often painted or covered in flat black.
Hope this helps. Good luck.