drivers window and convertible top

Ok guys..... first post here! I just picked a 200 Mustang convertible for my son. It is immaculate but has a few minor issues. It has a 5 speed trans and 3.8 V6. Runs great and drives great. The only real issue I can find with it is that when you close the drivers door with the window up, it doesn't go under the lip of the convertible top. It actually rides on the outside of the top. If you close the door by the glass, it will close perfectly. The doors don't sag or rattle at all. Is there any known fix for this issue? Oh BTW...... great site!

I had the door panel off already. I did find that the window was out of the clip on the back of the glass. I siliconed that back in place. Its almos like if the glass was down another 1/8" into the door, it would be perfect. There are several bolts holding the track in place. Tomorrow is stang day. It gets washed, clayed, polished and waxed. The interior is getting detailed and the leather is getting conditioned. I will also pull that door panel back off and see If I can lower the track a bit. The tilt of the glass looks perfect. It seals tight against the weatherstrip and doesn't leak a bit. The headlights also need a bit of restoration. They are not too awful bad, but they do have a bit of haze. New tires were put on it today as well as an alignment. I am currently researching an exhaust system for it to make it sound a little throaty. For a little V6 it's got plenty of get up and go, thanks to the 5 speed tranny.