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