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Hello, the first thing I would inspect is the driver side ground. It is under the driver side kick panel. If this ground is clean and tight then your concern is likely going to be a bad gem module. The gem module is located on the backside of the fuse panel. It controls all the items you have mentioned. The symptoms you have are common and similar to that of the gem module going bad.
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When you had it apart were there any signs of moisture inside the gem or fuse panel?
Did you swap only the gem module or did you swap over the entire fuse panel as well?
The driver side window is controlled through the gem module. The other windows aren't though. Beside the power for accessory delay.