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As some one who designs radio equipment, first I would like to say your not going to approach the receive sensitivity of your stock antenna located outside the car. The simple fact is the roof and support pillars are going to act like a shield and attenuate the signal.
Now that we have that established that There are several things that will have an effect on your radio reception. The key thing is matching your antenna impedance to your radios impedance. If you are going to use a loop antenna around the rear window it will work better or worse depending on which direction your car is facing. If your going to use a whip antenna it will work best normal to a ground plane. Also you want to make sure you have nothing close to the antenna as it will interfere with it (think iPhone4 boondoggle).
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