Dynamat and good seals and attachments shoudl keep any rattling to a minimum. I would definitely consider lining the back of the spare tire compartment with Dynamat (expensive as it is) to keep the boominess down to a minimum. A little foam behind your license plate will keep that from buzzing as you roll down the road.
A JL 8W3 won't need 400 watts of amp. Not that it's a bad thing, but you can get plenty of sound from 150 watts (depending on how you wire them - those speakers have dual voice coils, which allows you to adjust the load on the amp - but never mind that - have your installer figure it out) Good luck!
Swordy... you like the bass shakers? As much as the sound from a sub?