"Raising" the sills on the various MTL PS-1 boxcars won't solve the problem. The door height is correct even though the car height is exaggerated, so both of the door tracks are out of position. The roof remains too high even after Mike's modification, even though the model looks much better with the lower sills re-cut. There really is no way to make the model prototypical in one area that doesn't affect another area.
I think the high roof after modification is an artifact of my having only modified one side of the car in the photos and the underframe (and therefore the carbody) are skewed, tipping toward the camera.
But yes, the ends are still an issue, so it's not an ideal solution.