I reckon if the flywheel was loose you would know about it, shortly before it disappeared into orbit.
I doubt the flywheel would ever touch the cover plate, but the spigot on the end of the crank could if something flew up from the road and dinged the cover plate. Or it could be something else altogether causing the noise.
Another thought re your vibration issue - A worn pilot bushing can lead to vibration because it allows the clutch friction plate to go off centre and cause an imbalance.