[bobterry99]

I noticed that the window goes all the way up and down during the cycle of the soft top but when I press express down it sometimes goes down all the way and sometimes stops somewhere along the way. Would the limit switch cause this or is this a window switch issue?

I would suggest the limit switch is the most likely cause. Other possiblilities include damaged wiring from the switch to the soft top controller or the controller itself.

When you remove the door panel you should readily see the limit switch located in the bottom, middle of the door.