To tell you the truth, the install wasn't that bad. I just went slow and was meticulous with everything I did. As for the sound of the W3 vs the W6, I have not personally heard the W3's. My JL dealer told me that the W6 was the best at reproducing things such as snare drums, but also at delivering solid/tight bass in the lower frequencies.
The 4080 box is meant to slide in the corner of your trunk. It takes up a minimal amount of space and sounds great. I have seen custom boxes that go down under the trunk mat, but they are custom and are probably pretty $$$$$. The amp is mounted right on the back of the seat w/ some wood screws. I think one 500/1 amp is ok, but anything heavier might need some support.
Thanks for the heads up on the links... I'll have to search for them again and update accordingly. Let me know if you have any more questions.