Subframe Connectors, Torque Boxes & Inner Fender Braces

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Use wheel bearing grease in the tracks, and cover those doorhandle and lock rods with plastic tubing.
Those two things will deaden a lot of little rattles.

+1
I've used rubber vacuum tubing with a spiral slit but plastic should work too. If you replace your door plastic watershield with 2 layers of heavy weight roofing felt it dampens some noise also.