As a follow up to the original post, I dug through my wiring and found that I had indeed reversed my left channel output pair, resulting in phase problems. With the wiring corrected, the stereo image and bass response improved. A noticable difference.

So thanks for your help you guys, I will be applying this wisdom in the future.

The woofer I put in was a compact 16 cm (6 inch). It is pretty tiny, but it is about the only size I could get into the car (a Mini). It is currently running open-air with no enclosure, resting on the car floor. This has made quite a subtle difference to the listenability of the music of the car - I am finding at higher speeds, I am not having to jack up the volume so much.

So, on to 4 channels!