[Lynn Eades]

Rob, that seems massive! I know you have said the rear plate looks ok, but here's a few thoughts;
Put a straight edge against the rear hull and check it. Then if it does't look perfect,tighten up the tie back rods, pulling the motor back square, into the coupling, and then crack off the bolts holding the brake backing plates to the axle to see if anything moves? (I hope you have the drums off)
A quarter inch up at the front will likely mess up the exhaust pipes,the crank handle alignment, and probably worst of all, the fan blades under the radiator header tank.
Maybe when the motor was pulled the diff rotated up? With the coupling tight and the front mounts out, will the weight of the motor move it down?
As I said all just thoughts that might help
The Australians cleverly put a rubber mount at the rear with a flexible coupling.