I'm working on a 99 F350. The owner said he hasn't been able to activate the passenger window from the drivers side for a while. Now he run it down from the passenger side & it won't go up. We unplugged it and verified it had power on one side going up & the other side going down & it checked out. I figured it had to be motor, but after installing a new motor it still won't work. After reading a post on here we put power to one terminal at a time & put a chassis ground to the other & it works both ways. I tapped into the black wire going into the plug thinking that was ground & it definitely is. Not sure where to go from here?

 

Without actually physically checking everything, a good place to start would be to check the wiring between the door and pillar on both sides.
Those wire flex every time a door is opened and have been known to break in that location. You will need to open the rubber boot covering the wiring and carefully pull on each wire. If you find one that feels like pulling on spaghetti , you found the broken wire.You can make a temporary repair to get things working,but a more permanent repair will be necessary.