I would take the passenger door panel cover off(20 minutes max) just to see if you can find out what rattling.
If your windscreens are rattling just remove them,I noticed no change when I take mine out.
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-99' Zenith Blue 5-spd...didn't agree with a center divider on the freeway
-01' S Orient Red Metallic 6-spd...money pit...sold to buy a house
I have answer for #1, buy those plush tabs that are sold at stationary stores, they are used to place under table top items to prevent scratching, I placed them on every surface of the screens that touch the metal of the roll bar.
I was a little more permanent with the mesh screens, as I couldn't see any real reason to remove them often, so I used RTV (rubberized caulking) to mount them in place at the tabs... they're not going ANYWHERE now