1. I doubt you'll see much difference in the various JL amps in terms of SQ and that's not a power-hungry sub, so I'd just go with the XD300/1 (assuming you're set on JL amps).
2. Your wire placement would really depend on where you mount your sub enclosure and amp. However, it shouldn't be too much work, seeing as how all the wiring is already in your trunk. You'll just tap into the HK amp harness for your remote and for the signal out to a line out converter. I'll PM you a few links to get you started.
3. There's only so much you can do with the stock setup without gutting it and starting from scratch. A simple amp/sub addition will help fill in the lower end nicely, but you're still limited by the factory system components.