If the quarter panel install is as bad as you say it is, then I wouldn't worry so much about getting the door to line up with the quarter. Worry more about aligning the door with the rocker, as you need to have this correct before you try to cut off the quarter.
It sounds like the door striker is too high. Open up the door, look in the doorjamb, and you'll find a small oblong piece with two large phillips screws securing it to the doorjamb.
This striker can be moved in and out, up and down to affect how the door sits when it's closed. Don't loosen the screws up too much; you want to move the striker a little bit at a time. Trust me, a little movement can go a VERY long way. |