I would leave it up, and leave the hardtop off. But if you plan on driving it with the hardtop put it down, because you don't want to be lowering the top in temp.'s below around 50°, to put on the hardtop. Also, park it on some ply wood, and inflate the tires to avoid flat spots, and a car cover would be a good idea.
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1999 Ocean Blue Metallic Boxster - blueboxster.com
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