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A faulty ignition switch is known for many weird electrical gremlins, maybe it would affect top operation.
Another idea is the top relay. If you can find someone nearby that has the same relay model (I think they are different starting with year 2000 and up) you can do a quick swap and see if it works. Alternatively you can just buy an used relay for very cheap from Woody on here. I bought one from him and it fixed a problem I had.
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