Hi Babu,
The rattling of the top is often caused by lack of grease in the holes that the roof's stainless steel locking pins fit in to.
These holes are located near the top sides of the windshield. Pack them, and the rear ones, with Silicone grease, preferably Shin Etsu, available from Honda dealerships, and the rattling should completely stop.
DO NOT use Vaseline, as it is petroleum based, and will deteriorate the weatherstripping seals.
Can't be of any help regarding the gearbox, as I have never driven a Miata...................mostly looked at them IN MY REARVIEW MIRROR!
Cheers, Senior Sol