You are spot on right. If there is shaking, and it is waking you up it, sound proofing your bedroom alone won't help. Sound proofing is about eliminating noise that can potentially come in from within your home (say a running television etc).
It could involve
Having some kind of cone like structures on your walls that would prevent all echo
Putting easy ...
Some things you can do to calm annoying vibrations:
You could try just cleaning the flywheel. Of dirt. Might help.
Install a duct "skirt" "canvas duct connector" so that vibrations don't shake the structure as much.
You can try to "rebalance" your flywheel. Or replace it. Or replace it and the motor. Decreases vibrations.