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I would leave them off. Get the door to fit perfect without the rear striker mounted on the quarter panel. Then add the striker. It should close perfect. Now add your new aftermarket weather stripping and try and close the door. Usually it closes real hard now and you have to slam the heck out of it. It tears the w/s up at the top of the rear door on my 67. I would glue it in place and let it dry over night before closing the door. Now close it, it's hard to close. Just leave it and it will "wear in" and close better each time. My 2 cents
 
Yes you want to leave off the weatherstrip and the striker when you algin the door. If you have the weatherstrip on it can affect the lines because its not conformed to the shape of the quarter. If you have the striker on it can make the door "jump" up or down which in time can wear out the latch and the door bushings.

Once you have the door fitting like you want install the striker, but the trick is not to install it so the door fits flush with the quarter, leave it so the door fits past or sticks out. Install the weatherstrip, now close the door, you shouldnt have to slam it shut since you put the striker out so far. I do this because in a short awhile the weatherstrip will soften up and conform to its new shape especially if you leave the car sit in the sun for awhile. Once the weatherstrip softens up just move the striker back in. This method to me works so much better then slamming the door shut and forcing things to happen, just give it time...Eric

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1970 chevelle
1970 chevelle SS455 not a typo its a buick baby
1949 and 1972 chevy trucks
http://briefcase.yahoo.com/bc/sevt_chevelles
 
Excellent point Eric, I need to add that to my "Basics of Basics" on alignment.

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1965 Buick Gran Sport Convertible
1965 Buick Skylark H/T
"Fan of most anything that moves human beings"
 
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