Some folks replaced their sub with a Pioneer compact sub(model t-28c somthing). I looked for one given the recommendations here but couldn't find one and decided to let my ears decide.
After installing 652s and making the said adjustments I decided to keep my stock bose sub, but I did run dynamat around the edges where the sub attaches/touches the car. Not sure if the dynamat made things any better since the 652's provide good base. Didn't add any dynamat behind the sub either, in my 2002, there is a big thick chunk of insulate sound absorber behind the sub area already.
Over time I have found car subs loose their punch, due to either inadequate power, component lifespan or the elements. The latter two will most like impact bose since their speaker contruction seams cheap(imagine the sub as well, didn't look) and are all using paper-based cone construction. Some of the polypropolene speakers are problematic as well in colder climates(if its -5 don't crank the tunes, at least it was covered under warranty).
Steve...