Well I have some free time at work so I thought I'd enlighten you on somethings that I've learned from my venture of car audio fanatics...
JL SUCKS!! Every JL I heard sounds good at first, if you break them in right, but they tend to heat up ALOT and that sacrifices sound.
Ok now that i got that outta the way, I'd like to say alot of the "mainstream" brands (kicker, rockford fosgate, mtx, etc) are ok but overrated. From what you've said it sounds your more on the audiophile side, meaning you rather have music play the way it was meant to play, by that I mean weather its your right there in the concert, or in the studio. Best bet for SQ is Focal, Morel, or CDT (I heard CDT was good, never personally heard them tho). But since price is an issue to you, its gonna be hard to get the quality you want at a price where quality isn't really incorperated into the design of the sub/speakers.
MB Quartz, Eclipse, Memphis, and Pioneer makes some good subs for a low price.
Pioneer, Kenwood, and Hifonics makes good amps to match most subs.
If I was you, with the aftermarket factory setup, I'd have everything re-done, when I say that, it means pull out the factory sub, replace the head unit (sony has good HU for 100 or a little more, want something that has more options, poineer goes for around 199, the best??? Eclipse MKII for about 400) replace the wiring, add 2 amps (one for the speakers and one for the sub) add the sub of choice with box, and dyno that whole :q:q:q:qin car, it takes the driving noise away from inside the car and prevents any rattling from the exterior of the car.
All in all, if you just add a sub to the system, it'll sound wack in my opinion, but if you replace everything, speakers, HU, sub an amp, run your own wires, i think everytime you drive that car you'll be happy, cuz it sounds the way you want it
Just my thoughts on sound systems, im currently workin on my system and eventually when I start to re-do the system in the car, I'll have pictures of work in progress and finished product.