the base system is crap from end to end.
the speakers are the worse part of it. no matter what you do, its not going to sound decent until they are replaced.
the OEM head unit ain't no peach either, its much worse than the base audio systems in either the escape or focus platforms. yes all the new ford systems will heavily mess with the audio, mostly to protect the super crappy speakers they switched over to using. for the most part, the radio doesn't really start to mess with the audio signal until higher in the volume range. the bass roll off is the worse part of it. adding an amp will make a huge difference because you can have it set up to where it really sending a good amount of power with out having to turn the radio up too far and keep the signal closer to normal. a good amp interface like the AudioControl units that has a bass restoration circuit that only starts to add bass at the point the factory radio starts to pull it. even just a high level in basic mini amp like Alpines's Power Pack makes a huge difference.
if you are really serious, you can get near infinite tuning buy adding a stand alone DSP (or one built in to the amp), but you still will have the problem from above that a lot of DSPs wont adapt depending the volume level and you will want to set it up so that you're not having to crank the volume level up too far.
if you really think you have a wire than may have been pinned backwards in one of the harnesses (while extremely rare, it could be possible), the easiest way to find out for sure would be to call around all of the local audio shops and find one that has a polarity tester, since the test is super quick and easy, they should be able to test it for you and maybe only charge you for something like a 1/4 hour of shop time (cause the test really shouldn't take that long).
