Yeah, I would look in to using that FORScan utility with your OBD2 reader. Try to determine why the car is confused.
I think the window up/down signal is not coming from like a REAL SWITCH that you can test. I think it's a CANbus thing. So you can't really test it with continuity.
New update. I tested all of the wires from the SJB to the fuse box and also to the sensors and motors. All are good. Top Ajar sensor is reading correctly, all wires appear to have a good connection...but still nothing happens after the windows roll down. Even tried a different SJB, same results. Then, one final act of desperation, I but a jumper between the relay connections (UP Relay in place, Down Relay pulled and jumpered) and the top went down with no problem. Reversed the configuration and it went back up. So the motor is good.
All of this started when the back rear window motor died and I replaced it. Next step wil be to pull that back out and inspect it real close. Window works fine, but is it not sending the "window down" signal to the SJB? How can I test that?
FIXED IT!! I realized there is no physical switch to signal when the windows are down, but that signal is definitely a prerequisite for the SJB to activate the top down relay. So it must come from the window motor itself. I went back to the 2005 Mustang convertible at my local PIck-n-Pull and harvested the passenger rear window motor and regulator. Cleaned it up and plugged it in...IT WORKED! The top now goes up and down. The very first thing I fixed was putting in a brand new rear window motor. Because it worked the window properly, I thought all was good and moved on to testing other items. BUt I was fooled, the motor rolled the window up and down...but never sent the down signal to the SJB so the entire process stopped there. And the automotive store refunded my $150 for the new motor, while the harvested motor only cost me $30.
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