Re: Rear subs wiring gone?
I also have the same year Crossfire as yours but I have never seen a separate factory subwoofer wire you mention. It may exist on other models but someone here may confirm or deny that.
Of the two paralleled sets of Left and Right channels leading to the amp, I'm really not sure which set is used for the front speakers and which set is used for the rears, or subs as some may call it. I could test it on my XF if an opportunity arises for rewiring my amp.
But, yes. One of those sets are for the rear/sub channel as I believe the amp is four channels, Internally filtered. Two channels for low pass frequencies and two channels for high pass frequencies.