i have a 1999 Jetta and put in 2 12" subwoofers and had the same problem with the vibration. ive installed about 150 after-market stereos and subs and something all ways vibrates. what i did was took off the back sill and cut out foam and glued it to the back so that it would sit tight. put it back on and almost all of the vibration was gone. there are just a few trim pieces that rattle but that wont be a big deal. so if you can try that and see how it works.