Mounting the computer directly on the subwoofer assembly, again, poses the vibration problem. A solution might be to get some sound dampeners, or even some rubber grommets, to mount your hard drives and cd-roms on. This way, they act as insulators from the vibrations and allow your computer to function properly.
A way to test whether or not you are sufficiently insulating from vibrations is to take out your CDROM, and firmly place it on top of the subwoofer. Pop in a music CD, and crank the music. If your sound is skipping, you need more insulation.
I have a 400w system, and my computer was almost 4 feet away from my subwoofer, and I was still able to vibrate the whole thing causing skips. This is the magnitude you have to counter in order to safely operate your system.
Of course, you can always risk it, and build it anyways without sufficient protection. Though, if you happen to be reading/writing something on the HD, and playing loud music, you run the risk of physical sector damage, meaning parts of your HD disc are permanently unusable, causing corruption.