@ 600 dpi, 1 pixel = .0016"

That's pretty good. The problem comes from errors in reading the image. The edges of the parts are either rounded (out of focus) or not quite square to the scanner's rows.

I was able to draw the lines directly over the image. It may also be that the parts scanned actually have the mismatches as I've drawn them. Nothing every gets built exactly perfect.

If you look at the dimensions and compare one side to the other, they similar features should be sized and located by similar dimensions.

BTW. I'm not representing that drawing as final, it's a check print. I know there are errors. The most gross, is the depth of the cuts on the inner surfaces of the sides.