Okay, I'm going to start by disagreeing with almost everything offered, being a 2006 rig, I bet you do not have a Ford window lift motor, most likely a AM Equipment motor, whacking is for wackos, not motors, the manual is #888 and has full wiring schematics and a very good trouble shooting guide, Chris Bryant has a link on his web site, the motor is more likely bad than the gears, I will agree that they are a wink link, normally the steps hit the limit adjustment and the motor stops and there will be tension on the linkage and finally, monthly maintenance is good and not just when a problem arises.
So follow the trouble shooting guide and safety guidelines and you'll find the problem quickly.