Window alignment E46 coupe

I have an '02 325CI and the driver side window does not close correctly. I had the regulator replaced about a year ago. From inside the car, when closing the window all the way, it sounds
as if it hits the top hard. Also, when you have the window closed all the way and you shut the door, sometimes the last 4 inches of the top edge remain out of the track.You can see from the outside that the window didn't seat. Actually, when I can, I leave the car window open slightly to avoid this. From reading my "Bentley" I know it can be realigned, but would I be able to do it without special tools? After the last trip to my friendly neighborhood BMW dealer I needed $300 worth of body repair. I'd like to avoid a trip there again.
Thanks, Joe
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The window is supposed to drop about an inch when the door is opened, and then go up after the door is closed, sealing the window against the weatherstrip. I HAD an 02 M3 and the window only operated as it was supposed to about half the time. It was randomly operational. Numerous trips to MY dealer proved their ineptness at repair. The regulator was replaced under warranty, and the window "fit" was adjusted numerous times. Ultimately it was un-fixable and one of the reasons BMWNA bought the car back from me.
Just a note about my experiences (have owned nothing but BMWs since 1972). Dealer service "technicians" are usually incapable of making any adjustments correctly to body equipment. Body shops are even worse. Sadly I have had to live with some very annoying problems. At this point I am a believer that the dealers will most often just make things worse.
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To quote Bob Smitter:

Sadly Bob, I agree with you. I can't leave such a fine car in such incapable hands!!
Joe
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Same problem here on an '02 330 convertible. Happens mostly in cold weather, less often, if ever, in the summer.

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