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Do you have a voltmeter or simple 12 V test light and a reasonable knowledge of how to use them along with a wiring diagram? Just to clarify you replaced both the driver and passenger side switches with new ones and the window motor? Do the other windows work normally?
Stand By while I look up the wiring diagram and get some test procedures for you. I have to finish up and all get back to you in about 20 minutes.
IS this a double cab, access cab or standard cab?
At the passenger side power window switch does the blue wire with a red tracer have 12 volts to it? While probing the red wire with a black tracer and using the master window switch from the driver's door put the passenger window switch to the up position does the red wire with a black tracer at the passenger power window switch get 12 volts? And then put the passenger window to the down position from the drivers master control switch at that point does the red wire with a white tracer at the passenger window switch get 12 volts?
I will be monitoring on and off all day. Let me know how the test goes and make sure you have a good ground on your meter or test light.