If you take off the access panel for the top bolts there is two pieces of plastic that are on top of each other towards the right side. The outer panel and the inner one are making the noise. I put a piece of microfiber cloth between the two and solved the subwoofer vibration.
The sub rattle comes from the panel where the sub is. If you remove the access panel for soft top bolts there is two pieces of plastic that are right on top of each other(on the right side of access hole. I put a small piece of microfiber between them. rattle gone
It seems like my rattle is from the middle of the shocks. If you wiggle it the middle there is play between the piston and the housing it slides through