Shot in the dark here. If the upper engine harness connector is left unplugged the engine will still run but sound like all hell is breaking loose. Possibly the connector is not completely seated or locked in. But this also sets all kinds of codes. First time it happened to me it scared the crap out of me. Just grabbing for straws.
But I would'nt start tearing it apart just yet. If you cut the filter open and there's nothing in it, the bottom end should be fine. It could just be the counterweight on the dampner causing it to appear as though it's bouncing when it's really not. Easiest way to tell is cut open the filter and also see if you can move the dampner by hand up and down. Also stick a pry bar behnd the dampner and see if it moves in and out.