Windows and immobilizer?? I went thru some electrickery issues myself and didn't think they were connected.
The windows and the top are def linked and you should start to look at the top microswitch, the door latch micro switches etc.... This stuff is a real PIA. Check and clean all fuses first, then pull any relay and make sure it's the right one. We had mal-functioning wipers and it was the wrong relay. Looked right, had right plug but was wrong number. Got a voltmeter?? Check the switches for continuity, etc...
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Jon
1966 912, 1976 911
1986 944, 2000 Boxster
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