I've heard that the newest alpine S class subwoofers are very nice sounding, the alpine rep that checks in here has raved about their new 15". As far as amplifier goes, you seem to be on the right track with a D class as they won't be as hard on your charging system. There are alot of amps in your price range that can put out more power. I really like the looks of the Massive audio and PPI amps. They put a good amout of power out and have a very small footprint.
Don't overlook buying used from craigslist or the classifieds here, though. I've seen very nice amps locallly for good prices. The down side is that they aren't always as cosmetically correct, you may have to wait for a deal, and you need a way to test the function of the amplifier. If you have no experience with this it may be too intimidating. Patience can pay off, though, I got an old school phoenix gold amp last weekend that works great for $25. Not bad for an amp that is rated at 100w x2 @ 4 ohms and 400x1.