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That procedure would be good to know Visurveyor. According to Ford, if PATS is preventing a start, it will store a code and so will the PCM (P1260). I assume that the Ford information is correct. Also - if there is a PATS problem, this indicator will (should) either flash rapidly or glow steadily (for more than three seconds) when the ignition switch is turned to RUN or START.
IMO, it still could be related to the ignition switch and/or its wiring (which is then bypassed when you use the remote start wiring) ... If you haven't attempted the ignition troubleshooting suggestions, then they would be the next things to try. Anyway, we all have limited time and I can appreciate that for sure. Our goals are the same - for you to get it fixed as quickly as possible.
Thanks for sharing your knowledge and replying, it is appreciated. This sounds logical to me. Since the remote start (Autopage) works flawlessly and it still doesn't start with key. There was once recently it did, for fun I tried, but the next time I tried didn't work.
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