This 2004 Lincoln LS came in with the complaint that the power window does not work properly after replacing the power window regulator assembly. The window would not go down fully and when it was raised up it would immediately go back down to the position shown in the next picture. I should note that this vehicle has the auto up and auto down features for the power windows.
The first thing that has to be done before re-initialization can be done is that the motor has to be de-initialized. To do this two people are needed. First locate the power window main fuse located in the trunk fuse box under the floor covering. Then have you assistant turn the key on and depress the window switch fully to put the system into one touch mode. Next while the window is moving remove the fuse. This will de-initialize the motor. To initialize the motor make sure the key is off, install the fuse that was previously removed, turn the key on, depress the power window switch fully in the up position and hold until the glass stalls in the fully closed position for 2 seconds. Release the switch and the initialization is complete.. Note that if a new motor is installed it will only have to be initialized.
The window now closes and lowers correctly.