it's easy to spend tons of money in pursuit of sound quality (SQ). many find that the best thing to do is set a budget to work within and stick to it. and remember installation and tuning is just as important as the equipment you use, so budget in money for lots of sound deadening, wires, RCA cables, etc.
i would consider both JL audio and pioneer rev series components to be pretty good for that price range, but i definately love JL's amplifiers. they are often better than much pricier equipment ... excellent filters and power regulation.
rockford and kicker subwoofers tend to be designed with SPL (sound pressure level) in mind, rather than sound quality.
in my opinion, the best SQ for the dollar for components, coaxials and subs is CDT america. but keep in mind CDT's musical tonality tends to favor acoustic type music as in rock or jazz over synthetically produced sounds as in rap/hip-hop or techno/trance. if you prefer the synthetically produced music, a JL audio setup would be more suitable. here's a couple setups i considered for my own VX:
CDT...
CL-61A - 1/6.5" Components - $160
CL-4X - 4" Coaxials - $70
CL-1215S4 - 12" SVC Suwoofer - $100
JL Audio ...
XR650CSi - 1/6.6" Components - $260
TR400CXi - 4" Coaxials - $60
12W3V2D6 - 12" DVC Subwoofer - $180
i was planning to use a single multichannel amplifier for simplicity. JL audio's 500/5 amp uses hybrid class A/B circuitry for the fronts and rears and class D circuitry for the sub, so it's relatively small for the amount of power it produces. unfortunately, JL amps are not exactly cheap - $610 for this one.
anyway, those are my recommendations for a couple budget-minded SQ systems. i got the prices from wooferetc.com (my favorite online store).
it sounds like you're set on that USB feature, so i won't lecture you on the importance of a clean source signal for SQ, but i will say that using a head unit with 24-bit DAC's (digital to analog converters) goes a long way in terms of sound quality.