Thank you for the replies...the driver side switch has been giving me a little bit of trouble lately ( working intermittently sometimes on both windows), so I went ahead and ordered a new driver side pigtail and switch...I'm hoping that is the problem since like I said, it was working perfectly, and then after I removed and reinstalled the door panel, it stopped working. The motor was showing no signs of slowing down before this, and before I replaced the motor originally, i was getting 12 volts at the motor in the ACC position, and over 14 volts when the truck was running. If the new switch and pigtail don't fix it, I'll start looking into those other things.
Thanks!!