I have a 2006 convertible V6 and am having some issues with the rear quarter windows. I had to replace the regulator motor on the driver side quarter and now the windows aren't in sync. When both motors are plugged in (driver/passenger) the driver side won't go all the way up. If I unplug the passenger side then the driver side goes all the way up as it should. If I hold the window button up when both are plugged in, the driver side stops short and the passenger side will top out and then automatically go 3/4 of the way back down. Both windows will go all the way down when the button is pressed down. Because of this my convertible top wont go up and down either. I've been having to jump the relays in the fuse box to get the top to go up and down.

Is there a reset process for re-syncing the quarter windows back up? My ford dealership is worthless and they're about 200 cars deep before they'd be able to get to mine.

Thanks!