Actually both types of vibrations unfortunately!
I also need to replace the (makes a low frequency humming noise because it's old and probably worn out) CPU fan. Actually I've already purchased a Noctua "almost direct replacement" fan, but haven't gotten round to the hassle of connecting the new wires etc.
I agree with what you're saying about the side panel etc. I've for a long time been thinking about fixing it, but haven't found out exactly what kind of insulating material to use.
Unfortunately the OWC drive sleds aren't designed as precisely as Apple's, and because of this they physically touch the cMP side panel and transfers the vibrations, sometimes very loudly (but often stops (for a while) if I tap on the side panel).
Blue-tack might be usable, but I think something softer might be better. A rubber strip or something. Maybe
window sealing rubber strips which have double-sided tape on the back:
(image source:
DSf Ferreters)
As for the other noise: that's from inside the drives themselves. Unlike smaller drives (around 3GB or less in my experience), these high capacity "enterprise" drives have a much more powerful servo motor to position their drive heads. When the drive seeks you can definitely feel the movement. And this transfers to the rest of the computer, causing a lot of irritating "tick, tick, tick" sounds (especially when the 12TB Toshiba Time Machine drive starts taking backups).
The good news however is that when I've tried to attach the drive via SATA cables (instead of mounting with the drive sleds), and holding the drive in my hand almost all this noise goes away! So the good news is that it's mostly the vibrations that are transferred through metal that I hear.