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???? 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?
Remove the plate, clamp it level in a machinist's vice on your drill press, and check the holes for true (turned off, plunge the appropriately sized drill into the holes- the one(s) that will not let the drill plunge is/are off. Drill to oversize and Helicoil the offending hole(s) back to original size. Now it will all be nice and square.
Brewer's Performance - Mopar A833 4-Speed Transmission and Component Specialists (brewersperformance.com) and Brewers is Your Friend!