There is a table with what the motor with do based on the micro-switch states. Can't find it but will look for it. Seems like the switch for the clamshell it being depressed before the top closes? Perhaps the arm for from the transmission to the top needs to be extended? I'd disconnect the arms for the shell and carefully try to shut the top (making sure not to drive the transmissions too far).
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'98 Boxster 986
'87 911 Carrera Cabriolet
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