I put some closed cell weather strip down between the deck and the deck lid. That should keep it from vibrating against the deck, but maybe it's vibrating up against the window. I'll stuff a towel in there to test.
What push pins are you talking about? Got a pic?
I installed a 12inch sub in my cobalt several months ago. Since then, I've spent an ungodly amount of hours tracking down rattles and vibrations. I've replaced both front and rear factory speakers, padded the rear deck and trunk lid / floor with sound absorbing material, rerouted / secured any...