With the door in the up position, pull the harness towards the door and force a sharp bend in the harness right next to the door. The bend should place the harness below the hinge. Keeping it in that location install a heavy duty zip tie. The ones with the kit will not hold. This will prevent the harness from getting pinched between the door and the fender. It will also allow you to open the door more...
also, follow the the harness to the first connector that clips into the frame. There is a press in plug and a alignment pin to orient the plug horizontal. Cut off the alignment pin (both sides of the car) That will give the harness more movement with the hinge.