IF you only have, say, rust in the bottom 5" of the quarter, up to the weelhouse, your C piller, door jamb and trunk reveal area is good, you may find it easier to cut the new quarter down to a patch. Getting the gaps correct at the back glass and door jamb is time consuming. Also, sometimes the new metal stampings slip a bit in the die when they're made. Do not expect them to fit like a glove.
