You don't live terribly far from me if you ever want to come down and we can RTA the car. I live in Pepperell which is 2 hours if you drive the speed limit. I also have a 04 however it's currently in pieces.
The resonance problems…you might not have them at all. But it has nothing to do with your sub or crossover, it has to do with sealed fiberglass which likes to resonate depending on it's size at various frequencies. Your car deadening, trunk, rhino lining have nothing to do with it. If you do have the problems, they are very easy to fix. But putting your car on an RTA an analyzing what frequency problems you are having is very helpful as unless you have very good ears which comes from years of training and critical listening you probably won't notice them. But once they are gone (unless your hearing is not so good) People usually say…"hey…that sounds way better"
Amazing what not having 22 5db dips and humps can do.