the window height and sideward movement it controlled by 4 things inside your door. Take of the panel and you will find:
At the top, near the back and closer to the front, two brackets with a bolt in the top. The brackets shoudl have a felt piece on the end, which just touch the window when the window is rolled up. You can move these in and out to tighten the sideways movement of the door.
About 5 inches in from the back of the door, and again closer to the front, about 4 inches? down, there should be a bolth with a funny looking small tab coming out the top. this holds a big plastic thing that looks like a V. This controls how high the window is. The one at the front is a little different, but works the same.
You will have to play with these to ensure when the window is rolled up the entire way, it closes INSIDE the blowout clip, and sits properely.