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If your using aftermarket glass for the door, then thats your problem, they suck for those vehicles. You need to go OEM, I haven't had a problem with them since!
Those have enough adjustments that you should be able to adjust it out. you may need to adjust the bracket that the mirror attaches to. Also you can lay the topw of the door in some by loosening the top door hinge. IF all else fails tweak the metal track on the car body that the glass weatherstrip fits in. If you bend the metal out some on it it can hold more pressure on the back of the seal which will hold the seal tighter against the glass. hope that helps.