First the good news...
I received my test prints of the Lionel double door shims today, and evidently not only are the two ends different designs, but the bolsters are different distances from the end sills; only about the width of two human hairs, but enough to make me do some work...
So, one end has a nice 0.300" hole in the frame that I can use as a locator pin for the self alignment part, and that means only a single drill hole has to be put into the frame (center) and the rear hole in the Kadee box can just be screwed to the shim to prevent the box from rotating.
I had to redesign the other side, to set the shim the exact distance from the sill to the body bolster, and then add some width to align it in the center of the frame.
These come in 5-car sets, with 5 of each type of shim.
Atlas versus Lionel DD boxcar: