Usually clicking type noises from the window mean the gears are stripped. You'll have to pull the door panel and look at the gear on the motor and on the window actuator. It's mostlikely the teeth at the end of the motion when the window it nearly up, that are gone.
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Andrew '04 Jetta TDI Wagon
'82 300TD ~ Winnie ~ Sold '77 300D ~ Sold
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