Once the front track was done we layed the glass on the door to find the position of the front track. Another missed pic.
On mine we just drilled another set of holes for the front track. Brian's dad's truck he extended the mounting bracket to use the factory holes. I guess if your doors are already painted you may want to do that. The top will be held by the flexible track so it's just loose.
Here is is close to where it needed to be.