I don't have any experience with the Audiophile setup in the Expedition, but in the SVT focus, replacing the sub did a world of good. The factory 8 in the back just wasn't enough, it stopped getting louder at about 20 or so. Impressive for factory, but very easily made even more impressive.
As far as the cabins are concerned, we didn't change those out. They sounded pretty good as is. But, I could see how changing them out would really screw up the DSP, if you use it.