SL350 window won`t shut

I took off door panel to gain acsses to dent in door,had the dent removed i plugged in all the wiring refitted door panel, when i tryed the window it goes up and down but dosn`t shut like it should when you shut the door also quarter window is the same.
when i alarm the car using the fob the indicator lights don`t flash on and off but they do when dissarming could this be to do whith same problem as window.
any help would be appreciated thanks steve.