The idle speed is not supposed to be so low. The specifications mark that it must be between 1250 and 1500 RPM.
If the idle is very low, the knock you hear is caused by compression of the engine fighting against the inertia of the flywheel that keeps the engine running.
As for the vibration, I have no way of giving you accurate information. Maybe if you give us more information about the model year and mileage of your motorcycle, some of the most experienced members can help you.
Greetings from Mexico!
Only two things are infinite, the universe and human stupidity, and I'm not sure about the former. -Albert Einstein.
2007 Ninja 500R