Shifter Mounting Block Out of Whack

Threaded mounting holes for the shifter mechanism (Inland Type) are not straight and true. A straight edge across the centerlines of the holes shows no gaps, so I can only assume that at least one of the holes was not drilled/tapped right. I'm wondering if this has anything to do with the cracks in both of the shifter box mounting ears????
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I was considering just through-bolting the box to the plate with lock washers and jam nuts. A little bit of slack created by a slightly smaller bolt to fit through the tapped holes should allow the face of a new shifter box to hug up flush to the plate.

Any thoughts?