Paul:
If the knife back is straight in both planes, so that the sections are parallel to the cutter bar, then the guards must be out of line. You should be able to see that the guards are out of line when you sight down the points.John Deere guards are forged steel, so they are not harmed by a healthy blow from a heavy hammer to drive the guard up or down as required.
But I am a little confused; it seems the old sections did not have the clearance problems that the new ones have. That suggests that perhaps the guards are not out of line and that there is another problem.