personally i'd upgrade the hu and speakers but if you like the stock than leave it. for subs i'd look into a fi q, idmax, pair of dd 2512, 1 dd 3512, etc. depending on what you are going for (sq, sql, spl) that'll decide along with budget. 2 gauge will work fine. depending on your stock alt. you might want to get a bigger one, especially if you plan to run an amp to aftermarket speakers. at the minimum i'd do the big 3 and maybe a nice kinetik under the hood.
I think you are going to want some kind of a line driver if you are going to be using the stock HU, you will find that your not going to get a real clean signal from the speaker wires and a line out converter. Look into audiocontrol for a line driver with a built in equalizer/crossover. They have tons of models they should have something to suit your needs.
I agree with ctmike. Actually everybody has good advice, but Def dont get L7's unless you just want a sh*t load of bass. Pioneer has some cheap nice ones. A 1/2 Octave EQ in my book is always nice. It will def set off the high end. Unless that "Smart Rip" in your HU already has something similar. As for a box, thats outta my leage homie. .. . I've always been a fan of sealed or custom built band pass. But here I guess ported is pretty popular.
