It's difficult to picture the damage your are describing without a picture, but I can see your concerns. I should also point out that the hardtops have some flex/play in them, and tend to 'settle' to the car they are attached too. It takes a little while for them to readjust to a new car, and you can speed this up and reduce creaks and squeaks by adjusting the bolts on the sides (inside and above the lock levers).
To do this loosen the bolts and have someone push forward and down as hard they can while you tighten the bolts again. You may need to do it every few hundred miles until it settles, I think it took mine a couple months, but I am know noise free unless I go over a large bump or uneven curb.
If the top was infact stored improperly, like resting on the lock levers and the front corners, I would be a little weary. But again it's difficult to comment without seeing it. Best of luck!
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1999 Ocean Blue Metallic Boxster - blueboxster.com
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