I just finished installing my amp and subwoofer over the weekend, and I had this thread open in my laptop the whole time. Great write-up, thanks for the pics!
However, I did have to make a few changes to my installation...
Basically, I had 2 problems:
1. The remote wire was only giving me about 6 volts (unlike the 12 volts that are mentioned in the original post). I guess this is enough to power the stock amp, but my amp just laid there dead when my radio turned on. There are 2 solutions that you could use, either build a relay circuit (which means running additional wires from the battery to the back of the car), or you can cheat like I did and tap into the power socket / cigarette lighter in the luggage compartment. This works because the 12V power socket only comes on with the key at ACC or ON, so it's an easy fix.
2. The audio signal wires (thin black and white wires) that used to feed the stock amp were unfortunately not "plug-and-play" for my amp. Using a voltmeter, I found that the signal is carried with a 6V DC offset. So when I made my RCA connection, the (-) wire was being grounded to the chassis ground, and it was causing my rear speakers to buzz and hum. After much head scratching and bumper kicking, I found that the difference in grounds between my amp and my signal was causing the problem. I thought I needed a Speaker to line-in converter (as mentioned in the original post), but in fact all I needed was a ground loop isolator. I got mine at radio shack (ie The Source) for about $20, but I'm sure you can find them cheaper online if you don't mind waiting for shipping.
It's also worth noting that I mounted my amp inside the spare tire (i cut a round board and screwed my amp into that). Unfortunately, I couldn't really think of anywhere else to put it, but with all said and done, I like the Idea of being able to take my subwoofer out to use my whole trunk without having an amp in the way.
Now, with everything in place, everything's up and running and sounding great.