The 97 to 02 models have a plastic rear window that may crack if you raise or lower the roof in colder temperatures. It may also crack just due to being folded in half in the down postion if it gets really cold.
That said, I frequently will not use the car for a week at a time and have never had starting issues. I use a tender over the winter only. Your battery was already toast when you bought the car.
M~
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'99 black 986
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