I'm about to do a similar upgrade. I already have an Alpine 9851 head unit pulled from my Ranger, and I'm ordering the following:
Infinity Kappa 682.7cf front and rear, $300
Infinity Kappa 104.7W 10" sub wired for 2 ohms, $180
Under-seat box from eBay: $100
Alpine MRP-M650 600W amp, $300
or
Alpine MRD-M605 600W amp, $400
I listened to the Infinity, Alpine, Sony, JBL and other speakers in Best Buy, and I liked the sound of the Infinities the best of the lot, though Infinity, Alpine and JBL were all a close call. I didn't care for the Sony and Kenwood speakers personally, though this was too long ago for me to recall my specific reasons. I've never listend to any JL Audio stuff, but have heard good things, though I'm going to go with what I actually had a chance to audition in person.
I've always liked the sound of the Alpine amps, and I've always put together systems that were 100% in favor of sound quality, not decibels of boom. My sub will be in a small sealed box that will play lower and smoother, but not as loud as a ported or bandpass box. I had the Infinity Kappa Perfect 12.1D in my Ranger and it was awesome. Not super loud, but you could easily hear and feel stuff well below 30 Hz. If you're playing music for yourself, this is great. If you're trying to impress the ladies with your boom from 1/4-mile away, my system recommendation is not for you--you need to devote your whole back seat area to a huge, dual-12", high-wattage bandpass box for that.