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Each sliding door has their own motor. Disconnect the wiring to the little motor inside the door you want disabled.
Since the Freestar is just a Windstar with a different name, try the "Related Question" below for getting started with replacing the window motor.
There are a few "power motors" on a Windstar. Guessing the question might be referring to the window motor, see 'Related Questions" below for specifics about those...
I need to know the best way to remove and install the new window motor for a 96 Ford Windstar drivers side. Ray
Replacing 2002 Dodge power window motor driver side
Turn the door switch located at the front of the overhead console to off.
The engine may be reliable but there have been too many problems with power window switches,electric motors, power sliding doors and door ajar warning lights.
I had the same problem seems that the tumblers for the lock were seised up took it in to get it fix an was out in 15 mins.
If you are getting power to 2nd motor probably defective and needs replacing
The 1999 Ford Windstar owners manual shows : In the Power Distribution Box ( located in the engine compartment beside the battery ) * maxi fuse # 104 is a 40 amp fuse for the LH Power Seat Motors and LH Power Lumbar Motor *
Try replacing fuse 22 in the power distribution box next to the battery.
Sell the car without power sliding door , and buy one with.