Shut lines can be adjusted by removing the front and rear body shock pads then after the lines are good , make up some thinner/thicker pads to suit. Shut lines are one of the first things I look at on a show car. Its one of those things that are difficult to get right, swage line, door bottom, gaps, all these factors are not easy to get to look sharp and in line. Lets be honest, its a mass produced car, gaps were not always 100% right from the factory.
Been working on mine, and I know after its painted it will take a lot more work to get right. You are right that new door seals will affect, they do take time to bed in. These pics were taken with the old but still good door seals, striker and locks in place.