The arm can be bent. In fact the clam shell is probably bent too. The motor and transmissions can do all sorts of damage. On mine, most everything was bent. I still haven't gotten the passenger side to drop properly.
Also, check the alignment of the two transmissions the left one has the microswitches but if it doesn't stop at precisely the same time, top and clamshell can be out of synch.
I'm to the point that I'm considering taking it to a convertible friendly body shop to get things worked out.
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2001 Boxster
2007 Toyota Highlander
2003 New Beetle Convertible, Turbo, Tip 6 speed
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