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Is the Polk amplifier being used to power the highs, as well as the sub? If so it is likely that the remote turn on wire was just taken from an accessory wire such as the cigarette lighter, rather than the factory head unit's remote on, and it just goes off when the car is off, even is the stereo is still on. Best Buy likely would have just used a high level converter for the amplifier inputs, which are known to not produce the greatest sound quality. So, that may be the reason for 2 and 3. The best resolution for this would be to use the ******** harness (if you had the factory Boston Acoustic system) for the remote turn on and amplifier inputs, as this would likely fix all of your issues.
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