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On the 2000 and up models im pretty sure the microswitch in one of the transmissions keeps check if the top is up or down, and it checks transmissions position not motor. Im sure motor has nothing to do with it.. Try to do more research on the earlier models and see how your b pillar microswitch works, what exactly it checks.
But before that I'd try one more thing. Try to have the transmissions in full up position, if you say they have some markins and then try to remove the relay on the left side under the dash. Lookup "top relay" for our cars so you see where it is but its hard to miss as its a big bulky one. Try removing and putting it back with a ignition switch on and off, its part of the top mechanism and sometimes is even the issue for malfunctions. What I am hoping is maybe it will reset the light but its just a hope.
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